Enabling realtime logging in Toil
Deprecated toil method.  Please use "toil.lib.conversions.human2bytes()" instead."
Deprecated toil method.  Please use "toil.lib.conversions.human2bytes()" instead."
Cactus Command: /private/home/hickey/dev/cactus/venv-cactus-prism/bin/cactus-hal2chains ./js_chains8 ./8-t2t-apes-2023v2.hal ./8-t2t-apes-2023v2-chains --inMemory --bigChain --logFile ./8-t2t-apes-2023v2-chains.log --batchLogsDir batch-logs --batchSystem slurm --coordinationDir /data/tmp
Cactus Commit: 723b7899abe450d6e0872d87fcd6852dc155cb76
Importing ./8-t2t-apes-2023v2.hal
Batch system does not support auto-deployment. The user script ModuleDescriptor(dirPath='/private/home/hickey/dev/cactus/src', name='cactus.maf.cactus_hal2chains', fromVirtualEnv=False) will have to be present at the same location on every worker.
Running Toil version 6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96 on host mustard.
Starting real-time logging.
Issued job 'hal2chains_workflow' kind-hal2chains_workflow/instance-2iiaqsdd v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
0 jobs are running, 1 jobs are issued and waiting to run
2024-04-05 12:02:31.562633: Running the command: "axtChain"
2024-04-05 12:02:31.618545: Running the command: "faToTwoBit"
2024-04-05 12:02:31.640439: Running the command: "pslPosTarget"
2024-04-05 12:02:31.665787: Running the command: "hgLoadChain"
2024-04-05 12:02:31.727073: Running the command: "bedToBigBed"
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/c4b0/1b38/tmpaptve90f/8-t2t-apes-2023v2.hal
2024-04-05 12:03:41.173193: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/c4b0/1b38/tmpaptve90f/8-t2t-apes-2023v2.hal --tree"
2024-04-05 12:03:41.239626: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/c4b0/1b38/tmpaptve90f/8-t2t-apes-2023v2.hal --tree" in 0.065 seconds and 8.2 Mi memory
Got message from job at time 04-05-2024 12:03:41: Job used more disk than requested. For CWL, consider increasing the outdirMin requirement, otherwise, consider increasing the disk requirement. Job files/for-job/kind-hal2chains_get_genomes/instance-kj6ip5pg/cleanup/file-12ced34e475f4eb6bd72570a2260f372/stream used 828.10% disk (16.6 GiB [17783291904B] used, 2.0 GiB [2147483648B] requested).
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-2zzlu7pw v1 with job batch system ID: 2 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-dgtqj6mw v1 with job batch system ID: 3 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-ottvhkqz v1 with job batch system ID: 4 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-d3ip626s v1 with job batch system ID: 5 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-ob5xh3fy v1 with job batch system ID: 6 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-2uesl0xf v1 with job batch system ID: 7 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-qtebjov7 v1 with job batch system ID: 8 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_chrom_info' kind-hal2chains_chrom_info/instance-c948hn0b v1 with job batch system ID: 9 and disk: 19.9 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal
Computing chromosomes and 2bit ref sequence
2024-04-05 12:04:58.599645: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal --chromSizes GCA_028858775.2 | awk '{{print $1 "	0	" $2}}'"
Computing chromosomes and 2bit ref sequence
2024-04-05 12:04:58.647398: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal --chromSizes GCA_028878055.2 | awk '{{print $1 "	0	" $2}}'"
Computing chromosomes and 2bit ref sequence
Computing chromosomes and 2bit ref sequence
2024-04-05 12:04:58.682378: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal --chromSizes hs1 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:04:58.682033: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal --chromSizes GCA_028885625.2 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:04:58.838137: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal --chromSizes GCA_028858775.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.1585 seconds and 8.6 Mi memory
2024-04-05 12:04:58.847370: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal --chromSizes hs1 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.1589 seconds and 8.8 Mi memory
2024-04-05 12:04:58.847740: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal --chromSizes hs1"
2024-04-05 12:04:58.851403: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal --chromSizes GCA_028858775.2"
2024-04-05 12:04:58.856259: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal --chromSizes hs1" in 0.0077 seconds and 8.6 Mi memory
2024-04-05 12:04:58.859128: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal hs1 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/hs1.2bit"
2024-04-05 12:04:58.871396: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal --chromSizes GCA_028878055.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.1968 seconds and 8.6 Mi memory
2024-04-05 12:04:58.872635: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal --chromSizes GCA_028878055.2"
Computing chromosomes and 2bit ref sequence
2024-04-05 12:04:58.881462: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal --chromSizes GCA_028878055.2" in 0.008 seconds and 8.7 Mi memory
2024-04-05 12:04:58.881679: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal GCA_028878055.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/GCA_028878055.2.2bit"
2024-04-05 12:04:58.885856: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal --chromSizes GCA_028858775.2" in 0.01 seconds and 8.6 Mi memory
2024-04-05 12:04:58.886147: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal GCA_028858775.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/GCA_028858775.2.2bit"
2024-04-05 12:04:58.966444: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal --chromSizes GCA_028885625.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.2566 seconds and 8.7 Mi memory
2024-04-05 12:04:58.967716: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal --chromSizes GCA_028885625.2"
2024-04-05 12:04:58.977773: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal --chromSizes GCA_028885625.2" in 0.0092 seconds and 8.8 Mi memory
2024-04-05 12:04:58.977982: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal GCA_028885625.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/GCA_028885625.2.2bit"
2024-04-05 12:04:59.015118: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal --chromSizes GCA_028885655.2 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:04:59.112542: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal --chromSizes GCA_028885655.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.0859 seconds and 8.7 Mi memory
2024-04-05 12:04:59.119518: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal --chromSizes GCA_028885655.2"
2024-04-05 12:04:59.169824: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal --chromSizes GCA_028885655.2" in 0.0492 seconds and 8.8 Mi memory
2024-04-05 12:04:59.170120: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal GCA_028885655.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/GCA_028885655.2.2bit"
Computing chromosomes and 2bit ref sequence
2024-04-05 12:05:00.055370: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal --chromSizes GCA_029281585.2 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:05:00.083302: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal --chromSizes GCA_029281585.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.0208 seconds and 8.7 Mi memory
2024-04-05 12:05:00.084210: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal --chromSizes GCA_029281585.2"
2024-04-05 12:05:00.093274: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal --chromSizes GCA_029281585.2" in 0.0082 seconds and 8.6 Mi memory
2024-04-05 12:05:00.093537: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal GCA_029281585.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/GCA_029281585.2.2bit"
Computing chromosomes and 2bit ref sequence
2024-04-05 12:05:01.295269: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal --chromSizes GCA_029289425.2 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:05:01.570351: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal --chromSizes GCA_029289425.2 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.0201 seconds and 8.7 Mi memory
2024-04-05 12:05:01.572416: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal --chromSizes GCA_029289425.2"
2024-04-05 12:05:01.580060: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal --chromSizes GCA_029289425.2" in 0.007 seconds and 8.7 Mi memory
2024-04-05 12:05:01.580228: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal GCA_029289425.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/GCA_029289425.2.2bit"
Computing chromosomes and 2bit ref sequence
2024-04-05 12:05:11.826502: Running the command: "bash -c set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal --chromSizes hg38 | awk '{{print $1 "	0	" $2}}'"
2024-04-05 12:05:11.876650: Successfully ran: "bash -c 'set -eo pipefail && halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal --chromSizes hg38 | awk '"'"'{{print $1 "	0	" $2}}'"'"''" in 0.0487 seconds and 8.9 Mi memory
2024-04-05 12:05:11.877037: Running the command: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal --chromSizes hg38"
2024-04-05 12:05:11.887370: Successfully ran: "halStats /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal --chromSizes hg38" in 0.0095 seconds and 8.8 Mi memory
2024-04-05 12:05:11.887635: Running the command: "bash -c set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal hg38 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/hg38.2bit"
2024-04-05 12:07:20.645155: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/8-t2t-apes-2023v2.hal hs1 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/786e/b54a/tmp99ldqru4/hs1.2bit'" in 141.785 seconds and 1023.9 Mi memory
2024-04-05 12:07:24.261742: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/8-t2t-apes-2023v2.hal GCA_028878055.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/8558/b0b0/tmpxa6ra9fi/GCA_028878055.2.2bit'" in 145.379 seconds and 980.3 Mi memory
2024-04-05 12:07:24.772010: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/8-t2t-apes-2023v2.hal GCA_028858775.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4be1/34f2/tmp98ly6dma/GCA_028858775.2.2bit'" in 145.8749 seconds and 1021.5 Mi memory
2024-04-05 12:07:26.503460: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/8-t2t-apes-2023v2.hal GCA_028885655.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/913e/5d3f/tmp_qsbjgqg/GCA_028885655.2.2bit'" in 147.3321 seconds and 1.0 Gi memory
2024-04-05 12:07:27.034771: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/8-t2t-apes-2023v2.hal GCA_029289425.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/2636/b32f/tmph7hnqejq/GCA_029289425.2.2bit'" in 145.4537 seconds and 1.0 Gi memory
2024-04-05 12:07:30.608153: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/8-t2t-apes-2023v2.hal GCA_028885625.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/9092/933b/tmpdmlp2wv6/GCA_028885625.2.2bit'" in 151.6078 seconds and 1.0 Gi memory
2024-04-05 12:07:38.243172: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/8-t2t-apes-2023v2.hal GCA_029281585.2 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4f37/0694/tmp9s9kryoi/GCA_029281585.2.2bit'" in 158.1288 seconds and 1.1 Gi memory
2024-04-05 12:07:39.697072: Successfully ran: "bash -c 'set -eo pipefail && hal2fasta /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/8-t2t-apes-2023v2.hal hg38 | faToTwoBit stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/4dd7/8b23/tmpl_xk7ep7/hg38.2bit'" in 147.8084 seconds and 1.0 Gi memory
Issued job 'hal2chains_all' kind-hal2chains_all/instance-pvqti_ty v1 with job batch system ID: 10 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-ybx7ativ v1 with job batch system ID: 11 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-agwuebe8 v1 with job batch system ID: 12 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-biusvdrd v1 with job batch system ID: 13 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-6l1pdwlh v1 with job batch system ID: 14 and disk: 35.3 Gi, memory: 31.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-pak975bi v1 with job batch system ID: 15 and disk: 36.1 Gi, memory: 32.8 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-uags5kdx v1 with job batch system ID: 16 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-1glf0ciu v1 with job batch system ID: 17 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-wmrfcgit v1 with job batch system ID: 18 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-mvtsl8d_ v1 with job batch system ID: 19 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-h0nz1bl8 v1 with job batch system ID: 20 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-ber65qv2 v1 with job batch system ID: 21 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-e1sg_51e v1 with job batch system ID: 22 and disk: 35.6 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-7ymdiaa7 v1 with job batch system ID: 23 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-hontm48k v1 with job batch system ID: 24 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-bxhcmf5t v1 with job batch system ID: 25 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-7wb_2moa v1 with job batch system ID: 26 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-gss384ir v1 with job batch system ID: 27 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-git1scjr v1 with job batch system ID: 28 and disk: 36.2 Gi, memory: 32.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-k_5tcz30 v1 with job batch system ID: 29 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-64n246q8 v1 with job batch system ID: 30 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-hwwy1cer v1 with job batch system ID: 31 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-9rtbkr0s v1 with job batch system ID: 32 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-ey9a3fbc v1 with job batch system ID: 33 and disk: 35.1 Gi, memory: 31.8 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-t70bcxue v1 with job batch system ID: 34 and disk: 35.6 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-jgdki0jn v1 with job batch system ID: 35 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-u5xx53ko v1 with job batch system ID: 36 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-0a7c7aq9 v1 with job batch system ID: 37 and disk: 35.1 Gi, memory: 31.8 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-divnjvtn v1 with job batch system ID: 38 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-5chqua04 v1 with job batch system ID: 39 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-_wp_4kos v1 with job batch system ID: 40 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-ynt4j1wz v1 with job batch system ID: 41 and disk: 36.1 Gi, memory: 32.8 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-jgwivk6r v1 with job batch system ID: 42 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-iqnv42vc v1 with job batch system ID: 43 and disk: 35.3 Gi, memory: 31.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-cnmkksw9 v1 with job batch system ID: 44 and disk: 35.2 Gi, memory: 31.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-9p49asb_ v1 with job batch system ID: 45 and disk: 36.0 Gi, memory: 32.7 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-1l3rfzgq v1 with job batch system ID: 46 and disk: 35.6 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-nyvec4ta v1 with job batch system ID: 47 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-9ub1jvg7 v1 with job batch system ID: 48 and disk: 36.0 Gi, memory: 32.7 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-bemnu4lj v1 with job batch system ID: 49 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-854oqitd v1 with job batch system ID: 50 and disk: 35.7 Gi, memory: 32.4 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-q0ff6m5w v1 with job batch system ID: 51 and disk: 36.2 Gi, memory: 32.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-e2pnf655 v1 with job batch system ID: 52 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-hrlpz9ig v1 with job batch system ID: 53 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-9b00kvg4 v1 with job batch system ID: 54 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-6v68i8_t v1 with job batch system ID: 55 and disk: 35.2 Gi, memory: 31.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-awd51yoe v1 with job batch system ID: 56 and disk: 35.6 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-2qnd0p6k v1 with job batch system ID: 57 and disk: 35.7 Gi, memory: 32.4 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-9659xby9 v1 with job batch system ID: 58 and disk: 36.3 Gi, memory: 33.0 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-5nai7kk9 v1 with job batch system ID: 59 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-5duaxrxx v1 with job batch system ID: 60 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-l8ih7h2r v1 with job batch system ID: 61 and disk: 35.6 Gi, memory: 32.3 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-6sbbtseu v1 with job batch system ID: 62 and disk: 36.2 Gi, memory: 32.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-f87e8e5j v1 with job batch system ID: 63 and disk: 35.5 Gi, memory: 32.2 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-iahw6zof v1 with job batch system ID: 64 and disk: 35.4 Gi, memory: 32.1 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-l3ik4wt1 v1 with job batch system ID: 65 and disk: 36.2 Gi, memory: 32.9 Gi, cores: 1, accelerators: [], preemptible: False
Issued job 'hal2chains_genome' kind-hal2chains_genome/instance-bvzh98ij v1 with job batch system ID: 66 and disk: 35.3 Gi, memory: 32.0 Gi, cores: 1, accelerators: [], preemptible: False
Reading HAL file from job store to /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/8-t2t-apes-2023v2.hal
Reading HAL file from job store to /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/8-t2t-apes-2023v2.hal
Computing chains for query hg38 to target GCA_028885655.2
Computing chains for query hg38 to target GCA_028885625.2
Computing chains for query GCA_029289425.2 to target GCA_028878055.2
Computing chains for query hs1 to target GCA_028878055.2
Computing chains for query GCA_028885655.2 to target GCA_028885625.2
Computing chains for query GCA_028885655.2 to target GCA_029281585.2
Computing chains for query hs1 to target GCA_028885625.2
Computing chains for query GCA_028878055.2 to target GCA_028858775.2
Computing chains for query GCA_029281585.2 to target GCA_029289425.2
Computing chains for query GCA_028858775.2 to target GCA_028885625.2
Computing chains for query hg38 to target GCA_029281585.2
Computing chains for query hg38 to target GCA_028858775.2
Computing chains for query GCA_029289425.2 to target GCA_029281585.2
Computing chains for query GCA_028878055.2 to target GCA_028885625.2
Computing chains for query hg38 to target GCA_029289425.2
Computing chains for query hs1 to target GCA_028858775.2
Computing chains for query GCA_028878055.2 to target GCA_029289425.2
Computing chains for query GCA_029289425.2 to target GCA_028885625.2
Computing chains for query GCA_029281585.2 to target GCA_028878055.2
Computing chains for query hs1 to target GCA_029289425.2
Computing chains for query GCA_028885625.2 to target hg38
Computing chains for query GCA_028885655.2 to target hg38
Computing chains for query GCA_028858775.2 to target hs1
Computing chains for query GCA_029281585.2 to target GCA_028858775.2
2024-04-05 12:16:33.340772: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/8-t2t-apes-2023v2.hal hg38 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/hg38.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/GCA_028885655.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/hg38.2bit /dev/stdout | gzip"
Computing chains for query GCA_029289425.2 to target hs1
Computing chains for query GCA_028858775.2 to target GCA_029281585.2
Computing chains for query GCA_028885625.2 to target hs1
Computing chains for query GCA_028878055.2 to target hs1
Computing chains for query hg38 to target hs1
Computing chains for query GCA_029281585.2 to target hs1
Computing chains for query GCA_028885655.2 to target GCA_028878055.2
Computing chains for query GCA_028885625.2 to target GCA_028878055.2
Computing chains for query hs1 to target hg38
Computing chains for query GCA_028885625.2 to target GCA_028858775.2
Computing chains for query hs1 to target GCA_028885655.2
Computing chains for query GCA_029289425.2 to target hg38
Computing chains for query GCA_028885625.2 to target GCA_029289425.2
Computing chains for query hs1 to target GCA_029281585.2
Computing chains for query GCA_028878055.2 to target hg38
Computing chains for query GCA_028858775.2 to target hg38
Computing chains for query GCA_029281585.2 to target GCA_028885655.2
Computing chains for query hg38 to target GCA_028878055.2
Computing chains for query GCA_029281585.2 to target GCA_028885625.2
Computing chains for query GCA_028878055.2 to target GCA_028885655.2
Computing chains for query GCA_029289425.2 to target GCA_028858775.2
Computing chains for query GCA_028885655.2 to target GCA_029289425.2
Computing chains for query GCA_028878055.2 to target GCA_029281585.2
2024-04-05 12:16:34.628677: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029281585.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029289425.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.675714: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028878055.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028858775.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.723771: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_028885655.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_029281585.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.921336: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/8-t2t-apes-2023v2.hal hg38 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/hg38.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/GCA_028885625.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.922060: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885655.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885625.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.970372: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028858775.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028885625.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.986103: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_029289425.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_028878055.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:34.986211: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/8-t2t-apes-2023v2.hal hs1 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/hs1.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/GCA_028878055.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:35.444036: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/8-t2t-apes-2023v2.hal hs1 /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/hs1.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/GCA_028885625.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:35.444131: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_029281585.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_028858775.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:35.882099: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/GCA_029289425.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/hs1.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/GCA_029289425.2.2bit /dev/stdout | gzip"
Computing chains for query GCA_028858775.2 to target GCA_028885655.2
Computing chains for query GCA_028858775.2 to target GCA_028878055.2
Computing chains for query GCA_028885625.2 to target GCA_028885655.2
2024-04-05 12:16:38.194605: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_028878055.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.153721: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028878055.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028885625.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.245090: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/hg38.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/GCA_029281585.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.248016: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029289425.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029281585.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.266420: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/hg38.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/GCA_028858775.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.319180: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/hg38.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.429274: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_029289425.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_028885625.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.656912: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885625.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885655.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.758555: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028858775.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028885655.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.792701: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/8-t2t-apes-2023v2.hal hs1 /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/hs1.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/GCA_028858775.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.881310: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/8-t2t-apes-2023v2.hal hg38 /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hg38.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:39.939473: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/hs1.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.125486: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/GCA_028885625.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.134217: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/8-t2t-apes-2023v2.hal hs1 /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/hs1.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.262137: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/GCA_028885655.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/hg38.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.398482: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/GCA_028885625.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/hg38.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.515680: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_029281585.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_028878055.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.521221: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_028858775.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.544032: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028858775.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028878055.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.560776: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/GCA_028858775.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/hs1.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.600664: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/GCA_028878055.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.614152: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_028885655.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_029289425.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.798961: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/hs1.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:40.918978: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/8-t2t-apes-2023v2.hal hg38 /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/hg38.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/hg38.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.143404: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/GCA_028858775.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.193583: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hs1.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hs1.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.253743: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028885655.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.301371: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028885625.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.314944: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028885625.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028858775.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.379448: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_028878055.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.468537: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_028885625.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_029289425.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.593653: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028878055.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.646848: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/GCA_029289425.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.723591: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/GCA_028878055.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/GCA_028878055.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.729024: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_029289425.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_028858775.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.743540: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_029281585.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:41.962398: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_029281585.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_028885625.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:42.305341: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/GCA_029281585.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/GCA_029281585.2.2bit /dev/stdout | gzip"
Computing chains for query GCA_028858775.2 to target GCA_029289425.2
Computing chains for query GCA_029281585.2 to target hg38
Computing chains for query GCA_029289425.2 to target GCA_028885655.2
Computing chains for query GCA_028885655.2 to target hs1
Computing chains for query GCA_028885655.2 to target GCA_028858775.2
Computing chains for query GCA_028885625.2 to target GCA_029281585.2
2024-04-05 12:16:47.715838: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_028858775.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_029289425.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_028858775.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:47.738076: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_028885625.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_029281585.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_028885625.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:47.872294: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028885655.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028858775.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:47.956508: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_029289425.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_028885655.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_029289425.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:49.166417: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/GCA_028885655.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/hs1.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/GCA_028885655.2.2bit /dev/stdout | gzip"
2024-04-05 12:16:49.323378: Running the command: "bash -c set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/GCA_029281585.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/hg38.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/GCA_029281585.2.2bit /dev/stdout | gzip"
2024-04-05 12:42:12.400511: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/8-t2t-apes-2023v2.hal hg38 /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hg38.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/f545/tmpxtzq0u8l/hg38.2bit /dev/stdout | gzip'" in 1532.5168 seconds and 6.8 Gi memory
2024-04-05 12:42:12.463160: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.chain.gz"
2024-04-05 12:42:12.560144: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.chain.gz" in 0.0961 seconds and 1.9 Mi memory
2024-04-05 12:42:12.560430: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.chain"
2024-04-05 12:42:13.169968: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.chain" in 0.6087 seconds and 74.0 Mi memory
2024-04-05 12:42:13.170252: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 12:42:13.256164: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.0851 seconds and 3.8 Mi memory
2024-04-05 12:42:13.256383: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.bb"
2024-04-05 12:42:13.452450: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.bb" in 0.1954 seconds and 10.9 Mi memory
2024-04-05 12:42:13.452666: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 12:42:14.989003: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 1.5356 seconds and 8.0 Mi memory
2024-04-05 12:42:14.989236: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.link.bb"
2024-04-05 12:42:17.220409: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/fbab/40e1/tmpndw5ihg6/hs1_vs_hg38.bigChain.link.bb" in 2.2304 seconds and 22.2 Mi memory
2024-04-05 12:44:41.675530: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hs1.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/1723/tmp2li54pr4/hs1.2bit /dev/stdout | gzip'" in 1680.4806 seconds and 6.8 Gi memory
2024-04-05 12:44:41.716955: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.chain.gz"
2024-04-05 12:44:41.826945: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.chain.gz" in 0.1089 seconds and 1.8 Mi memory
2024-04-05 12:44:41.827383: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.chain"
2024-04-05 12:44:42.472852: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.chain" in 0.6445 seconds and 75.3 Mi memory
2024-04-05 12:44:42.473228: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 12:44:42.557446: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.0833 seconds and 3.8 Mi memory
2024-04-05 12:44:42.557721: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.bb"
2024-04-05 12:44:42.807412: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.bb" in 0.2488 seconds and 11.0 Mi memory
2024-04-05 12:44:42.807843: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 12:44:44.448944: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 1.6402 seconds and 8.0 Mi memory
2024-04-05 12:44:44.449215: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.link.bb"
2024-04-05 12:44:46.865587: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/561b/a82d/tmpay6fxugw/hg38_vs_hs1.bigChain.link.bb" in 2.4155 seconds and 22.4 Mi memory
54 jobs are running, 0 jobs are issued and waiting to run
2024-04-05 13:07:27.165658: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885655.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885625.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/18a2/tmp38eh661y/GCA_028885655.2.2bit /dev/stdout | gzip'" in 3052.2402 seconds and 9.0 Gi memory
2024-04-05 13:08:23.193218: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885625.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885655.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/f13a/tmpi2gbbems/GCA_028885625.2.2bit /dev/stdout | gzip'" in 3103.5347 seconds and 9.1 Gi memory
2024-04-05 13:11:34.688486: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_028858775.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_029289425.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/1242/tmp9r7dbrcs/GCA_028858775.2.2bit /dev/stdout | gzip'" in 3286.9714 seconds and 8.3 Gi memory
2024-04-05 13:15:24.073194: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.chain.gz"
2024-04-05 13:15:24.103059: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.chain.gz"
2024-04-05 13:15:24.349369: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.chain.gz" in 0.275 seconds and 1.7 Mi memory
2024-04-05 13:15:24.349784: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.chain"
2024-04-05 13:15:24.418966: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.chain.gz" in 0.3148 seconds and 1.8 Mi memory
2024-04-05 13:15:24.419324: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.chain"
2024-04-05 13:15:26.277674: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.chain" in 1.927 seconds and 233.3 Mi memory
2024-04-05 13:15:26.278104: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 13:15:26.440997: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.chain" in 2.021 seconds and 241.6 Mi memory
2024-04-05 13:15:26.441319: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 13:15:26.438074: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1591 seconds and 3.6 Mi memory
2024-04-05 13:15:26.438337: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 13:15:26.575469: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1335 seconds and 3.8 Mi memory
2024-04-05 13:15:26.575672: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 13:15:26.903096: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.bb" in 0.4639 seconds and 11.9 Mi memory
2024-04-05 13:15:26.903514: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 13:15:27.013026: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.bb" in 0.4367 seconds and 13.0 Mi memory
2024-04-05 13:15:27.013380: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 13:15:32.350542: Running the command: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.chain.gz"
2024-04-05 13:15:32.641998: Successfully ran: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.chain.gz" in 0.2902 seconds and 1.8 Mi memory
2024-04-05 13:15:32.642341: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.chain"
2024-04-05 13:15:33.483265: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 6.5789 seconds and 7.8 Mi memory
2024-04-05 13:15:33.483552: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 13:15:33.876063: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 6.862 seconds and 7.9 Mi memory
2024-04-05 13:15:33.876297: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 13:15:34.581869: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.chain" in 1.9388 seconds and 235.9 Mi memory
2024-04-05 13:15:34.582155: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 13:15:34.757220: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1744 seconds and 3.7 Mi memory
2024-04-05 13:15:34.757452: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 13:15:35.264410: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.bb" in 0.5063 seconds and 12.2 Mi memory
2024-04-05 13:15:35.264950: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 13:15:41.449256: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/09cd/61a3/tmpkhazjwi1/GCA_028885625.2_vs_GCA_028885655.2.bigChain.link.bb" in 7.9648 seconds and 62.5 Mi memory
2024-04-05 13:15:41.731434: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 6.4657 seconds and 7.9 Mi memory
2024-04-05 13:15:41.731670: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 13:15:42.339230: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/1d59/eeda/tmp0t3xvr5y/GCA_029289425.2_vs_GCA_028858775.2.bigChain.link.bb" in 8.4622 seconds and 56.6 Mi memory
2024-04-05 13:15:49.618421: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/b8d3/1855/tmppm_onfdh/GCA_028885655.2_vs_GCA_028885625.2.bigChain.link.bb" in 7.886 seconds and 60.6 Mi memory
2024-04-05 13:21:55.129328: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_029289425.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_028858775.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/45ea/tmpxip8q3uy/GCA_029289425.2.2bit /dev/stdout | gzip'" in 3913.3984 seconds and 8.7 Gi memory
2024-04-05 13:21:55.185749: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.chain.gz"
2024-04-05 13:21:55.556376: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.chain.gz" in 0.3695 seconds and 1.7 Mi memory
2024-04-05 13:21:55.556824: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.chain"
2024-04-05 13:21:57.887310: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.chain" in 2.3295 seconds and 242.7 Mi memory
2024-04-05 13:21:57.887740: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 13:21:58.050732: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1621 seconds and 3.8 Mi memory
2024-04-05 13:21:58.051013: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 13:21:58.596005: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.bb" in 0.544 seconds and 12.8 Mi memory
2024-04-05 13:21:58.596419: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 13:22:06.566283: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 7.9689 seconds and 8.0 Mi memory
2024-04-05 13:22:06.566559: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 13:22:16.550623: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9984/570e/tmp9x4y0niz/GCA_028858775.2_vs_GCA_029289425.2.bigChain.link.bb" in 9.9831 seconds and 54.9 Mi memory
50 jobs are running, 0 jobs are issued and waiting to run
2024-04-05 14:00:47.892934: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/hg38.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/4df9/tmpo9gf2gd2/hg38.2bit /dev/stdout | gzip'" in 6248.5724 seconds and 13.1 Gi memory
2024-04-05 14:00:47.966598: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.chain.gz"
2024-04-05 14:00:48.359758: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.chain.gz" in 0.3922 seconds and 1.9 Mi memory
2024-04-05 14:00:48.360157: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.chain"
2024-04-05 14:00:51.179135: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.chain" in 2.8181 seconds and 309.3 Mi memory
2024-04-05 14:00:51.179469: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:00:51.314782: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1345 seconds and 3.8 Mi memory
2024-04-05 14:00:51.315040: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.bb"
2024-04-05 14:00:51.698268: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.bb" in 0.3825 seconds and 11.3 Mi memory
2024-04-05 14:00:51.698643: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:01:01.542447: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 9.843 seconds and 7.9 Mi memory
2024-04-05 14:01:01.542677: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.link.bb"
2024-04-05 14:01:14.049511: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/c852/3662/tmptxquqjrs/GCA_029289425.2_vs_hg38.bigChain.link.bb" in 12.506 seconds and 75.2 Mi memory
2024-04-05 14:02:11.690497: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/8-t2t-apes-2023v2.hal hs1 /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/hs1.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/edc3/tmpi22fd_8c/hs1.2bit /dev/stdout | gzip'" in 6331.5547 seconds and 13.2 Gi memory
2024-04-05 14:02:11.752307: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.chain.gz"
2024-04-05 14:02:12.141500: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.chain.gz" in 0.3882 seconds and 1.8 Mi memory
2024-04-05 14:02:12.141861: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.chain"
2024-04-05 14:02:14.947813: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.chain" in 2.8052 seconds and 305.1 Mi memory
2024-04-05 14:02:14.948140: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:02:15.078152: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1292 seconds and 3.7 Mi memory
2024-04-05 14:02:15.078386: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.bb"
2024-04-05 14:02:15.425643: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.bb" in 0.3465 seconds and 11.3 Mi memory
2024-04-05 14:02:15.426009: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:02:25.289568: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 9.8628 seconds and 8.0 Mi memory
2024-04-05 14:02:25.289797: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.link.bb"
2024-04-05 14:02:38.349560: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1f7e/e870/tmpaijdpga7/GCA_029289425.2_vs_hs1.bigChain.link.bb" in 13.0589 seconds and 75.5 Mi memory
2024-04-05 14:05:46.747397: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/8-t2t-apes-2023v2.hal hs1 /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/hs1.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/GCA_028858775.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/3a7c/tmpgnmftjsm/hs1.2bit /dev/stdout | gzip'" in 6546.953 seconds and 13.2 Gi memory
2024-04-05 14:05:46.804082: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.chain.gz"
2024-04-05 14:05:47.158512: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.chain.gz" in 0.3535 seconds and 1.7 Mi memory
2024-04-05 14:05:47.158861: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.chain"
2024-04-05 14:05:49.751400: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.chain" in 2.5918 seconds and 309.4 Mi memory
2024-04-05 14:05:49.751741: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:05:49.870586: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1181 seconds and 3.7 Mi memory
2024-04-05 14:05:49.870817: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.bb"
2024-04-05 14:05:50.221477: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.bb" in 0.3499 seconds and 12.5 Mi memory
2024-04-05 14:05:50.221821: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:05:55.998473: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/hg38.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/GCA_028858775.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/5653/tmplcz5_fxe/hg38.2bit /dev/stdout | gzip'" in 6556.7308 seconds and 13.1 Gi memory
2024-04-05 14:05:56.045069: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.chain.gz"
2024-04-05 14:05:56.430701: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.chain.gz" in 0.3847 seconds and 1.8 Mi memory
2024-04-05 14:05:56.431083: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.chain"
2024-04-05 14:05:59.227930: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.chain" in 2.796 seconds and 308.5 Mi memory
2024-04-05 14:05:59.228259: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:05:59.267985: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 9.0455 seconds and 7.8 Mi memory
2024-04-05 14:05:59.268212: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.link.bb"
2024-04-05 14:05:59.349858: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1209 seconds and 3.8 Mi memory
2024-04-05 14:05:59.350055: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.bb"
2024-04-05 14:05:59.694976: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.bb" in 0.3443 seconds and 11.3 Mi memory
2024-04-05 14:05:59.695213: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:06:09.542608: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 9.8467 seconds and 7.9 Mi memory
2024-04-05 14:06:09.542867: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.link.bb"
2024-04-05 14:06:10.725213: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0706/5cef/tmpycc2yca4/GCA_028858775.2_vs_hs1.bigChain.link.bb" in 11.4562 seconds and 76.1 Mi memory
2024-04-05 14:06:22.585008: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/8485/d787/tmpld59in33/GCA_028858775.2_vs_hg38.bigChain.link.bb" in 13.0413 seconds and 75.0 Mi memory
2024-04-05 14:12:15.424930: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/GCA_029289425.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/hs1.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/3c16/tmp9c95badf/GCA_029289425.2.2bit /dev/stdout | gzip'" in 6939.5414 seconds and 13.1 Gi memory
2024-04-05 14:12:15.495154: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.chain.gz"
2024-04-05 14:12:15.860385: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.chain.gz" in 0.3643 seconds and 1.8 Mi memory
2024-04-05 14:12:15.860766: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.chain"
2024-04-05 14:12:18.464933: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.chain" in 2.6033 seconds and 304.8 Mi memory
2024-04-05 14:12:18.465249: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:12:18.587676: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1218 seconds and 3.7 Mi memory
2024-04-05 14:12:18.587913: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 14:12:18.923341: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.bb" in 0.3347 seconds and 11.5 Mi memory
2024-04-05 14:12:18.923712: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:12:27.200881: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 8.2764 seconds and 8.0 Mi memory
2024-04-05 14:12:27.201109: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 14:12:38.290844: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/db35/dfb6/tmpduzp6woj/hs1_vs_GCA_029289425.2.bigChain.link.bb" in 11.089 seconds and 72.5 Mi memory
2024-04-05 14:22:45.336757: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/GCA_028858775.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/hs1.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/6963/tmp5_ug6slj/GCA_028858775.2.2bit /dev/stdout | gzip'" in 7564.7744 seconds and 13.1 Gi memory
2024-04-05 14:22:46.054773: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.chain.gz"
2024-04-05 14:22:46.458268: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.chain.gz" in 0.4022 seconds and 1.8 Mi memory
2024-04-05 14:22:46.458660: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.chain"
2024-04-05 14:22:47.318802: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/GCA_029289425.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/861f/tmpwqvqez_7/GCA_029289425.2.2bit /dev/stdout | gzip'" in 7565.6703 seconds and 13.2 Gi memory
2024-04-05 14:22:47.983535: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.chain.gz"
2024-04-05 14:22:48.358037: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.chain.gz" in 0.3731 seconds and 1.8 Mi memory
2024-04-05 14:22:48.358430: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.chain"
2024-04-05 14:22:49.255453: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.chain" in 2.796 seconds and 308.3 Mi memory
2024-04-05 14:22:49.255786: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:22:49.368409: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1118 seconds and 3.8 Mi memory
2024-04-05 14:22:49.368640: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 14:22:49.731720: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.bb" in 0.3623 seconds and 12.3 Mi memory
2024-04-05 14:22:49.732090: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:22:50.884873: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.chain" in 2.5256 seconds and 309.3 Mi memory
2024-04-05 14:22:50.885235: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:22:51.164712: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.2787 seconds and 3.7 Mi memory
2024-04-05 14:22:51.164910: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 14:22:51.529220: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.bb" in 0.3637 seconds and 11.3 Mi memory
2024-04-05 14:22:51.529449: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:22:58.850957: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 9.1181 seconds and 8.0 Mi memory
2024-04-05 14:22:58.851192: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 14:22:59.856677: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 8.3265 seconds and 8.0 Mi memory
2024-04-05 14:22:59.856939: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 14:23:10.772104: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/86a5/2630/tmprqyzqqdx/hg38_vs_GCA_029289425.2.bigChain.link.bb" in 10.9143 seconds and 72.9 Mi memory
2024-04-05 14:23:11.114738: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/0e0f/b027/tmpcb5k3mcu/hs1_vs_GCA_028858775.2.bigChain.link.bb" in 12.2627 seconds and 72.9 Mi memory
2024-04-05 14:25:04.242049: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029281585.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029289425.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/cc8d/tmp8pdtcd11/GCA_029281585.2.2bit /dev/stdout | gzip'" in 7709.612 seconds and 15.8 Gi memory
2024-04-05 14:25:04.818728: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.chain.gz"
2024-04-05 14:25:05.263529: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.chain.gz" in 0.4438 seconds and 1.8 Mi memory
2024-04-05 14:25:05.263865: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.chain"
2024-04-05 14:25:08.548521: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.chain" in 3.284 seconds and 378.3 Mi memory
2024-04-05 14:25:08.548846: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:25:08.694778: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1452 seconds and 3.9 Mi memory
2024-04-05 14:25:08.695021: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 14:25:09.117366: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.bb" in 0.4217 seconds and 11.5 Mi memory
2024-04-05 14:25:09.117744: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:25:20.343939: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 11.2254 seconds and 7.9 Mi memory
2024-04-05 14:25:20.344199: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 14:25:34.378326: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/730f/681c/tmpwwzc0_y4/GCA_029289425.2_vs_GCA_029281585.2.bigChain.link.bb" in 14.0333 seconds and 90.3 Mi memory
2024-04-05 14:26:23.215457: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_028878055.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/2cbd/tmpy6636pc1/GCA_028878055.2.2bit /dev/stdout | gzip'" in 7781.834 seconds and 16.1 Gi memory
2024-04-05 14:26:23.278367: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.chain.gz"
2024-04-05 14:26:23.884200: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.chain.gz" in 0.6048 seconds and 1.8 Mi memory
2024-04-05 14:26:23.884603: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.chain"
2024-04-05 14:26:29.845163: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.chain" in 5.9597 seconds and 572.8 Mi memory
2024-04-05 14:26:29.845542: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:26:29.945551: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.099 seconds and 3.8 Mi memory
2024-04-05 14:26:29.945803: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 14:26:30.311921: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.bb" in 0.3652 seconds and 10.8 Mi memory
2024-04-05 14:26:30.312336: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:26:56.664513: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 26.3512 seconds and 8.0 Mi memory
2024-04-05 14:26:56.664781: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 14:27:17.364896: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/GCA_028858775.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/7fe2/tmp4xm8ul2p/GCA_028858775.2.2bit /dev/stdout | gzip'" in 7836.2195 seconds and 13.1 Gi memory
2024-04-05 14:27:17.423578: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.chain.gz"
2024-04-05 14:27:17.776002: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.chain.gz" in 0.3513 seconds and 1.7 Mi memory
2024-04-05 14:27:17.776392: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.chain"
2024-04-05 14:27:18.984244: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/b138/4c5c/tmpyjxvkkte/GCA_029281585.2_vs_GCA_028878055.2.bigChain.link.bb" in 22.3184 seconds and 76.3 Mi memory
2024-04-05 14:27:20.257356: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.chain" in 2.4801 seconds and 308.2 Mi memory
2024-04-05 14:27:20.257743: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:27:20.370176: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1115 seconds and 3.7 Mi memory
2024-04-05 14:27:20.370446: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 14:27:20.704042: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.bb" in 0.3327 seconds and 11.2 Mi memory
2024-04-05 14:27:20.704439: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:27:28.840142: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 8.1348 seconds and 8.0 Mi memory
2024-04-05 14:27:28.840385: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 14:27:39.800475: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/f28a/706f/tmp3iq9cxk_/hg38_vs_GCA_028858775.2.bigChain.link.bb" in 10.959 seconds and 73.1 Mi memory
2024-04-05 14:28:26.192121: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_029281585.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_028858775.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/c8b7/tmpzmjcpaiy/GCA_029281585.2.2bit /dev/stdout | gzip'" in 7910.7467 seconds and 15.8 Gi memory
2024-04-05 14:28:26.254031: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.chain.gz"
2024-04-05 14:28:26.697089: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.chain.gz" in 0.4422 seconds and 1.8 Mi memory
2024-04-05 14:28:26.697466: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.chain"
2024-04-05 14:28:29.973778: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.chain" in 3.2756 seconds and 379.9 Mi memory
2024-04-05 14:28:29.974127: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:28:30.109047: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1341 seconds and 3.7 Mi memory
2024-04-05 14:28:30.109259: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 14:28:30.496536: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.bb" in 0.3866 seconds and 11.4 Mi memory
2024-04-05 14:28:30.496842: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:28:41.842349: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 11.3448 seconds and 7.9 Mi memory
2024-04-05 14:28:41.842582: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 14:28:55.930928: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/5900/fe4d/tmpsndmk3hq/GCA_028858775.2_vs_GCA_029281585.2.bigChain.link.bb" in 14.0876 seconds and 90.5 Mi memory
2024-04-05 14:34:04.709653: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028878055.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028885625.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/9251/tmp_qaqvt2d/GCA_028878055.2.2bit /dev/stdout | gzip'" in 8245.5545 seconds and 16.2 Gi memory
2024-04-05 14:34:04.789270: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.chain.gz"
2024-04-05 14:34:05.470046: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.chain.gz" in 0.6798 seconds and 1.8 Mi memory
2024-04-05 14:34:05.470420: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.chain"
2024-04-05 14:34:10.782209: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.chain" in 5.311 seconds and 566.7 Mi memory
2024-04-05 14:34:10.782560: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:34:10.883721: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1003 seconds and 3.8 Mi memory
2024-04-05 14:34:10.883959: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 14:34:11.183938: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.bb" in 0.2991 seconds and 11.3 Mi memory
2024-04-05 14:34:11.184301: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:34:29.957049: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.7719 seconds and 7.9 Mi memory
2024-04-05 14:34:29.957298: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 14:34:52.237882: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/cf80/1e14/tmpzbo303v4/GCA_028885625.2_vs_GCA_028878055.2.bigChain.link.bb" in 22.2798 seconds and 75.6 Mi memory
2024-04-05 14:36:04.648294: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028878055.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e387/tmprjto2mbp/GCA_028878055.2.2bit /dev/stdout | gzip'" in 8362.9826 seconds and 16.3 Gi memory
2024-04-05 14:36:04.723331: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.chain.gz"
2024-04-05 14:36:05.328110: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.chain.gz" in 0.6036 seconds and 1.7 Mi memory
2024-04-05 14:36:05.328538: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.chain"
2024-04-05 14:36:09.917063: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.chain" in 4.5877 seconds and 565.8 Mi memory
2024-04-05 14:36:09.917416: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:36:10.008693: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.0905 seconds and 3.8 Mi memory
2024-04-05 14:36:10.008943: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 14:36:10.277747: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.bb" in 0.2678 seconds and 11.4 Mi memory
2024-04-05 14:36:10.278143: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:36:27.045667: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.7667 seconds and 8.0 Mi memory
2024-04-05 14:36:27.045923: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 14:36:46.963773: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/0887/e67c/tmpwg5wajc3/GCA_028885655.2_vs_GCA_028878055.2.bigChain.link.bb" in 19.917 seconds and 75.2 Mi memory
2024-04-05 14:42:12.939711: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_028858775.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/7498/tmprh7_fo5m/GCA_028858775.2.2bit /dev/stdout | gzip'" in 8732.417 seconds and 15.8 Gi memory
2024-04-05 14:42:13.107261: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.chain.gz"
2024-04-05 14:42:13.580169: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.chain.gz" in 0.4718 seconds and 1.8 Mi memory
2024-04-05 14:42:13.580509: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.chain"
2024-04-05 14:42:17.080390: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.chain" in 3.499 seconds and 379.9 Mi memory
2024-04-05 14:42:17.080709: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:42:17.224433: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1429 seconds and 3.8 Mi memory
2024-04-05 14:42:17.224654: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 14:42:17.692937: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.bb" in 0.4675 seconds and 12.8 Mi memory
2024-04-05 14:42:17.693293: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:42:29.909066: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 12.2149 seconds and 7.9 Mi memory
2024-04-05 14:42:29.909295: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 14:42:45.156434: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/95d0/82a0/tmpezfdbcq6/GCA_029281585.2_vs_GCA_028858775.2.bigChain.link.bb" in 15.2463 seconds and 91.1 Mi memory
2024-04-05 14:45:32.573579: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/hs1.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/GCA_029281585.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/d6d7/tmp3rdc4sih/hs1.2bit /dev/stdout | gzip'" in 8931.7724 seconds and 15.6 Gi memory
2024-04-05 14:45:32.720784: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.chain.gz"
2024-04-05 14:45:33.146772: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.chain.gz" in 0.4249 seconds and 1.9 Mi memory
2024-04-05 14:45:33.147172: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.chain"
2024-04-05 14:45:36.156687: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.chain" in 3.0086 seconds and 371.3 Mi memory
2024-04-05 14:45:36.157031: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:45:36.290718: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.133 seconds and 3.7 Mi memory
2024-04-05 14:45:36.290896: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.bb"
2024-04-05 14:45:36.713541: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.bb" in 0.422 seconds and 13.1 Mi memory
2024-04-05 14:45:36.713808: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:45:47.574626: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 10.8601 seconds and 7.9 Mi memory
2024-04-05 14:45:47.574865: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.link.bb"
2024-04-05 14:46:01.041415: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/50e6/f64f/tmpudfia8l7/GCA_029281585.2_vs_hs1.bigChain.link.bb" in 13.4657 seconds and 88.7 Mi memory
2024-04-05 14:49:17.034215: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_029281585.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_028878055.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/aebb/tmp3kzyv3go/GCA_029281585.2.2bit /dev/stdout | gzip'" in 9156.5168 seconds and 16.7 Gi memory
2024-04-05 14:49:17.244460: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.chain.gz"
2024-04-05 14:49:17.932178: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.chain.gz" in 0.6866 seconds and 1.8 Mi memory
2024-04-05 14:49:17.932571: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.chain"
2024-04-05 14:49:23.169650: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.chain" in 5.2362 seconds and 574.1 Mi memory
2024-04-05 14:49:23.169994: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:49:23.273221: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1024 seconds and 3.8 Mi memory
2024-04-05 14:49:23.273450: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 14:49:23.577175: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.bb" in 0.303 seconds and 11.0 Mi memory
2024-04-05 14:49:23.577561: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:49:42.670138: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 19.0918 seconds and 8.0 Mi memory
2024-04-05 14:49:42.670365: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 14:50:05.406939: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/57c4/8fe0/tmpebzcxsvg/GCA_028878055.2_vs_GCA_029281585.2.bigChain.link.bb" in 22.7357 seconds and 63.9 Mi memory
2024-04-05 14:50:05.573896: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/GCA_029281585.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/hg38.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/63a3/tmpjeq_lwf7/GCA_029281585.2.2bit /dev/stdout | gzip'" in 9196.2491 seconds and 15.3 Gi memory
2024-04-05 14:50:05.899441: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.chain.gz"
2024-04-05 14:50:06.339955: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.chain.gz" in 0.4396 seconds and 1.8 Mi memory
2024-04-05 14:50:06.340316: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.chain"
2024-04-05 14:50:07.758622: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029289425.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029281585.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/47b3/tmpddl6qsn0/GCA_029289425.2.2bit /dev/stdout | gzip'" in 9208.5087 seconds and 15.8 Gi memory
2024-04-05 14:50:07.946162: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.chain.gz"
2024-04-05 14:50:08.454543: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.chain.gz" in 0.5074 seconds and 1.8 Mi memory
2024-04-05 14:50:08.454931: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.chain"
2024-04-05 14:50:09.477561: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.chain" in 3.1365 seconds and 377.8 Mi memory
2024-04-05 14:50:09.477880: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:50:09.629586: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1511 seconds and 3.8 Mi memory
2024-04-05 14:50:09.629783: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 14:50:10.082837: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.bb" in 0.4525 seconds and 11.4 Mi memory
2024-04-05 14:50:10.083097: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:50:12.123877: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.chain" in 3.6681 seconds and 378.4 Mi memory
2024-04-05 14:50:12.124208: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:50:12.294481: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1695 seconds and 3.7 Mi memory
2024-04-05 14:50:12.294710: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 14:50:12.779929: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.bb" in 0.4846 seconds and 11.2 Mi memory
2024-04-05 14:50:12.780201: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:50:20.359055: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 10.2753 seconds and 7.9 Mi memory
2024-04-05 14:50:20.359276: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 14:50:25.943329: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 13.1624 seconds and 8.0 Mi memory
2024-04-05 14:50:25.943589: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 14:50:33.815049: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/79af/5f41/tmp0wcznfhn/hg38_vs_GCA_029281585.2.bigChain.link.bb" in 13.4551 seconds and 85.6 Mi memory
2024-04-05 14:50:42.296019: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/bd97/4248/tmpn4l13ahm/GCA_029281585.2_vs_GCA_029289425.2.bigChain.link.bb" in 16.3516 seconds and 90.9 Mi memory
2024-04-05 14:52:18.480022: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/8-t2t-apes-2023v2.hal hg38 /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/hg38.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/GCA_029281585.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/b7ea/tmp8edkgstq/hg38.2bit /dev/stdout | gzip'" in 9339.2336 seconds and 15.5 Gi memory
2024-04-05 14:52:18.686687: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.chain.gz"
2024-04-05 14:52:19.193370: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.chain.gz" in 0.5056 seconds and 1.8 Mi memory
2024-04-05 14:52:19.193732: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.chain"
2024-04-05 14:52:22.790925: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.chain" in 3.5964 seconds and 376.6 Mi memory
2024-04-05 14:52:22.791456: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:52:22.966618: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1744 seconds and 3.8 Mi memory
2024-04-05 14:52:22.966870: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.bb"
2024-04-05 14:52:23.515146: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.bb" in 0.5475 seconds and 13.1 Mi memory
2024-04-05 14:52:23.515528: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:52:36.321191: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 12.8049 seconds and 8.0 Mi memory
2024-04-05 14:52:36.321436: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.link.bb"
2024-04-05 14:52:52.333041: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2efc/c218/tmpbhgwf939/GCA_029281585.2_vs_hg38.bigChain.link.bb" in 16.0107 seconds and 88.3 Mi memory
2024-04-05 14:58:03.165246: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/GCA_029281585.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/c17d/tmp8vtshbw7/GCA_029281585.2.2bit /dev/stdout | gzip'" in 9680.8583 seconds and 15.3 Gi memory
2024-04-05 14:58:03.369785: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.chain.gz"
2024-04-05 14:58:03.796462: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.chain.gz" in 0.4256 seconds and 1.8 Mi memory
2024-04-05 14:58:03.796856: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.chain"
2024-04-05 14:58:06.818696: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.chain" in 3.021 seconds and 371.6 Mi memory
2024-04-05 14:58:06.819061: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 14:58:06.950897: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1311 seconds and 3.7 Mi memory
2024-04-05 14:58:06.951124: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 14:58:07.383748: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.bb" in 0.4319 seconds and 12.7 Mi memory
2024-04-05 14:58:07.384136: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 14:58:17.480517: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 10.0956 seconds and 8.0 Mi memory
2024-04-05 14:58:17.480771: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 14:58:30.682607: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/d79e/419a/tmpumxqnm2n/hs1_vs_GCA_029281585.2.bigChain.link.bb" in 13.201 seconds and 84.5 Mi memory
30 jobs are running, 0 jobs are issued and waiting to run
2024-04-05 15:14:40.591972: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028885655.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/2c4f/tmplasawn64/GCA_028885655.2.2bit /dev/stdout | gzip'" in 10679.3365 seconds and 16.6 Gi memory
2024-04-05 15:14:41.052319: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.chain.gz"
2024-04-05 15:14:41.671350: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.chain.gz" in 0.6177 seconds and 1.8 Mi memory
2024-04-05 15:14:41.671758: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.chain"
2024-04-05 15:14:46.353847: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.chain" in 4.6813 seconds and 568.5 Mi memory
2024-04-05 15:14:46.354205: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:14:46.467910: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1129 seconds and 3.7 Mi memory
2024-04-05 15:14:46.468151: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 15:14:46.799680: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.bb" in 0.3307 seconds and 11.5 Mi memory
2024-04-05 15:14:46.800078: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:15:03.782000: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.9811 seconds and 7.9 Mi memory
2024-04-05 15:15:03.782238: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 15:15:08.897738: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_029281585.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_028885625.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/f5d9/tmpmdam53x3/GCA_029281585.2.2bit /dev/stdout | gzip'" in 10706.9336 seconds and 18.9 Gi memory
2024-04-05 15:15:08.972627: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.chain.gz"
2024-04-05 15:15:09.561756: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.chain.gz" in 0.5881 seconds and 1.8 Mi memory
2024-04-05 15:15:09.562141: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.chain"
2024-04-05 15:15:14.028471: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.chain" in 4.4655 seconds and 540.2 Mi memory
2024-04-05 15:15:14.028832: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:15:14.142120: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1125 seconds and 3.7 Mi memory
2024-04-05 15:15:14.142358: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 15:15:14.513969: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.bb" in 0.3708 seconds and 12.5 Mi memory
2024-04-05 15:15:14.514378: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:15:23.878224: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/8ca6/534a/tmpvfmfjc4l/GCA_028878055.2_vs_GCA_028885655.2.bigChain.link.bb" in 20.0952 seconds and 63.7 Mi memory
2024-04-05 15:15:30.544605: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.0294 seconds and 8.0 Mi memory
2024-04-05 15:15:30.544879: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 15:15:51.112025: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31e/c9cc/tmpvzf8raed/GCA_028885625.2_vs_GCA_029281585.2.bigChain.link.bb" in 20.5663 seconds and 134.8 Mi memory
2024-04-05 15:18:06.908044: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028885625.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/0463/tmp0367_ijz/GCA_028885625.2.2bit /dev/stdout | gzip'" in 10885.6049 seconds and 16.6 Gi memory
2024-04-05 15:18:07.365379: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.chain.gz"
2024-04-05 15:18:07.979983: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.chain.gz" in 0.6133 seconds and 1.8 Mi memory
2024-04-05 15:18:07.980360: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.chain"
2024-04-05 15:18:12.597046: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.chain" in 4.6159 seconds and 569.3 Mi memory
2024-04-05 15:18:12.597408: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:18:12.707119: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1089 seconds and 3.8 Mi memory
2024-04-05 15:18:12.707368: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 15:18:13.033314: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.bb" in 0.3251 seconds and 11.2 Mi memory
2024-04-05 15:18:13.033700: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:18:29.815020: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.7805 seconds and 8.0 Mi memory
2024-04-05 15:18:29.815268: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 15:18:31.066210: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/8-t2t-apes-2023v2.hal GCA_029281585.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_029281585.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/bfef/tmp1ymj_imd/GCA_029281585.2.2bit /dev/stdout | gzip'" in 10909.3211 seconds and 18.9 Gi memory
2024-04-05 15:18:31.143101: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.chain.gz"
2024-04-05 15:18:31.734006: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.chain.gz" in 0.5898 seconds and 1.9 Mi memory
2024-04-05 15:18:31.734435: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.chain"
2024-04-05 15:18:36.230057: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.chain" in 4.4948 seconds and 545.6 Mi memory
2024-04-05 15:18:36.230415: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:18:36.344921: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1138 seconds and 3.7 Mi memory
2024-04-05 15:18:36.345105: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.bb"
2024-04-05 15:18:36.723897: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.bb" in 0.3781 seconds and 12.5 Mi memory
2024-04-05 15:18:36.724265: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:18:49.877343: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2c9c/a20b/tmpow_lynh7/GCA_028878055.2_vs_GCA_028885625.2.bigChain.link.bb" in 20.0612 seconds and 63.9 Mi memory
2024-04-05 15:18:53.140102: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.4151 seconds and 7.9 Mi memory
2024-04-05 15:18:53.140359: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.link.bb"
2024-04-05 15:19:13.865957: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/de11/6ed3/tmp2fc6fbez/GCA_028885655.2_vs_GCA_029281585.2.bigChain.link.bb" in 20.7248 seconds and 135.4 Mi memory
2024-04-05 15:20:05.056958: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_028885625.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_029281585.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/b758/tmpbowd19l7/GCA_028885625.2.2bit /dev/stdout | gzip'" in 10997.3174 seconds and 18.7 Gi memory
2024-04-05 15:20:05.130994: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.chain.gz"
2024-04-05 15:20:05.713481: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.chain.gz" in 0.5814 seconds and 1.9 Mi memory
2024-04-05 15:20:05.713857: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.chain"
2024-04-05 15:20:10.118313: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.chain" in 4.4037 seconds and 540.5 Mi memory
2024-04-05 15:20:10.118645: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:20:10.235041: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1157 seconds and 3.8 Mi memory
2024-04-05 15:20:10.235254: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 15:20:10.575430: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.bb" in 0.3396 seconds and 11.2 Mi memory
2024-04-05 15:20:10.575687: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:20:26.616794: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.0405 seconds and 8.0 Mi memory
2024-04-05 15:20:26.617026: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 15:20:32.993035: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_028885655.2.bed GCA_029281585.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_029281585.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/2fce/tmphbj3rfp1/GCA_028885655.2.2bit /dev/stdout | gzip'" in 11038.2643 seconds and 18.8 Gi memory
2024-04-05 15:20:33.078942: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.chain.gz"
2024-04-05 15:20:34.032621: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.chain.gz" in 0.9524 seconds and 1.7 Mi memory
2024-04-05 15:20:34.033087: Running the command: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.chain"
2024-04-05 15:20:40.952482: Successfully ran: "hgLoadChain -noBin -test GCA_029281585.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.chain" in 6.9184 seconds and 546.1 Mi memory
2024-04-05 15:20:40.952922: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:20:41.109175: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1554 seconds and 3.8 Mi memory
2024-04-05 15:20:41.109472: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 15:20:41.743368: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.bb" in 0.6331 seconds and 11.2 Mi memory
2024-04-05 15:20:41.743802: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:20:47.141483: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/99e0/a39e/tmpbe_o9s5c/GCA_029281585.2_vs_GCA_028885625.2.bigChain.link.bb" in 20.5237 seconds and 135.9 Mi memory
2024-04-05 15:21:07.449870: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 25.7053 seconds and 7.9 Mi memory
2024-04-05 15:21:07.450151: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 15:21:41.184546: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/03b8/405d/tmpywrrj9jh/GCA_029281585.2_vs_GCA_028885655.2.bigChain.link.bb" in 33.7335 seconds and 136.4 Mi memory
2024-04-05 15:39:41.227210: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028858775.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028878055.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/6027/tmpaej8mez5/GCA_028858775.2.2bit /dev/stdout | gzip'" in 12180.6814 seconds and 22.5 Gi memory
2024-04-05 15:39:41.349890: Running the command: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.chain.gz"
2024-04-05 15:39:41.994363: Successfully ran: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.chain.gz" in 0.6435 seconds and 1.8 Mi memory
2024-04-05 15:39:41.994712: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.chain"
2024-04-05 15:39:46.937925: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.chain" in 4.9425 seconds and 598.7 Mi memory
2024-04-05 15:39:46.938255: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:39:47.378306: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.4394 seconds and 3.6 Mi memory
2024-04-05 15:39:47.378496: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 15:39:47.696500: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.bb" in 0.3175 seconds and 12.1 Mi memory
2024-04-05 15:39:47.696761: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:40:05.760572: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.0631 seconds and 7.9 Mi memory
2024-04-05 15:40:05.760819: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 15:40:27.131720: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/bc58/bedd/tmpyg33kj3n/GCA_028878055.2_vs_GCA_028858775.2.bigChain.link.bb" in 21.3701 seconds and 67.1 Mi memory
2024-04-05 15:40:33.047742: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028878055.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028858775.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/6f8e/tmprv2q98pk/GCA_028878055.2.2bit /dev/stdout | gzip'" in 12238.3705 seconds and 22.0 Gi memory
2024-04-05 15:40:33.211698: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.chain.gz"
2024-04-05 15:40:33.859868: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.chain.gz" in 0.6472 seconds and 1.8 Mi memory
2024-04-05 15:40:33.860159: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.chain"
2024-04-05 15:40:38.987704: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.chain" in 5.1269 seconds and 597.3 Mi memory
2024-04-05 15:40:38.988026: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:40:39.072239: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.0836 seconds and 3.6 Mi memory
2024-04-05 15:40:39.072443: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 15:40:39.318036: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.bb" in 0.2449 seconds and 11.2 Mi memory
2024-04-05 15:40:39.318368: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:40:57.672647: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.3536 seconds and 8.0 Mi memory
2024-04-05 15:40:57.672854: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 15:41:19.224127: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/33b0/8b46/tmpcg__ktpx/GCA_028858775.2_vs_GCA_028878055.2.bigChain.link.bb" in 21.5505 seconds and 79.1 Mi memory
2024-04-05 15:57:31.381645: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_029289425.2.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_028878055.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/1e04/tmpymkg8a8s/GCA_029289425.2.2bit /dev/stdout | gzip'" in 13256.3931 seconds and 22.5 Gi memory
2024-04-05 15:57:32.664562: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.chain.gz"
2024-04-05 15:57:33.791420: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.chain.gz" in 1.1255 seconds and 1.8 Mi memory
2024-04-05 15:57:33.791919: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.chain"
2024-04-05 15:57:43.983828: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.chain" in 10.1908 seconds and 598.1 Mi memory
2024-04-05 15:57:43.984336: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:57:44.225364: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.2399 seconds and 3.7 Mi memory
2024-04-05 15:57:44.225689: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 15:57:44.826949: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.bb" in 0.6002 seconds and 11.2 Mi memory
2024-04-05 15:57:44.827434: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:58:24.363837: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 39.5346 seconds and 7.9 Mi memory
2024-04-05 15:58:24.364152: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 15:59:05.756593: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/af2d/50d1/tmpgbryz_8h/GCA_028878055.2_vs_GCA_029289425.2.bigChain.link.bb" in 41.3913 seconds and 67.1 Mi memory
2024-04-05 15:59:32.634271: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/8-t2t-apes-2023v2.hal hg38 /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/hg38.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/GCA_028878055.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/1c6a/tmpnrzq6esv/hg38.2bit /dev/stdout | gzip'" in 13371.7134 seconds and 22.3 Gi memory
2024-04-05 15:59:32.740232: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.chain.gz"
2024-04-05 15:59:33.389274: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.chain.gz" in 0.648 seconds and 1.8 Mi memory
2024-04-05 15:59:33.389665: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.chain"
21 jobs are running, 0 jobs are issued and waiting to run
2024-04-05 15:59:38.469602: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.chain" in 5.0791 seconds and 611.8 Mi memory
2024-04-05 15:59:38.469943: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 15:59:38.573912: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1033 seconds and 3.7 Mi memory
2024-04-05 15:59:38.574108: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.bb"
2024-04-05 15:59:38.870787: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.bb" in 0.2961 seconds and 11.4 Mi memory
2024-04-05 15:59:38.871053: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 15:59:57.133435: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.2617 seconds and 7.8 Mi memory
2024-04-05 15:59:57.133689: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.link.bb"
2024-04-05 16:00:18.817799: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/9555/f2c8/tmpb5ngjtcw/GCA_028878055.2_vs_hg38.bigChain.link.bb" in 21.6833 seconds and 66.8 Mi memory
2024-04-05 16:01:39.654429: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_028878055.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_029289425.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/cbf3/tmpew9qssfz/GCA_028878055.2.2bit /dev/stdout | gzip'" in 13501.4357 seconds and 22.0 Gi memory
2024-04-05 16:01:39.754328: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.chain.gz"
2024-04-05 16:01:40.501501: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.chain.gz" in 0.7459 seconds and 1.8 Mi memory
2024-04-05 16:01:40.501915: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.chain"
2024-04-05 16:01:46.323842: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.chain" in 5.8211 seconds and 596.6 Mi memory
2024-04-05 16:01:46.324180: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:01:46.444859: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1199 seconds and 3.8 Mi memory
2024-04-05 16:01:46.445055: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 16:01:46.750193: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.bb" in 0.3045 seconds and 10.8 Mi memory
2024-04-05 16:01:46.750488: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:02:07.976846: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 21.2256 seconds and 8.0 Mi memory
2024-04-05 16:02:07.977097: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 16:02:32.757654: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/2c97/026e/tmpuxltbgn1/GCA_029289425.2_vs_GCA_028878055.2.bigChain.link.bb" in 24.7797 seconds and 79.0 Mi memory
2024-04-05 16:10:19.066845: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028858775.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028885655.2.2bit /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/c0e3/tmpt943nzvg/GCA_028858775.2.2bit /dev/stdout | gzip'" in 14019.3068 seconds and 24.6 Gi memory
2024-04-05 16:10:19.177129: Running the command: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.chain.gz"
2024-04-05 16:10:19.789226: Successfully ran: "gzip -dc /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.chain.gz" in 0.6112 seconds and 1.9 Mi memory
2024-04-05 16:10:19.789544: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.chain"
2024-04-05 16:10:24.439767: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.chain" in 4.6495 seconds and 567.0 Mi memory
2024-04-05 16:10:24.440072: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:10:24.560752: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.12 seconds and 3.7 Mi memory
2024-04-05 16:10:24.560965: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 16:10:24.919611: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/bigChain.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.bb" in 0.358 seconds and 12.4 Mi memory
2024-04-05 16:10:24.919902: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:10:42.203597: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 17.283 seconds and 8.0 Mi memory
2024-04-05 16:10:42.203823: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 16:10:49.477047: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_029289425.2.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_028885655.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/37fc/tmp8wt0c7ae/GCA_029289425.2.2bit /dev/stdout | gzip'" in 14041.519 seconds and 24.5 Gi memory
2024-04-05 16:10:49.605979: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.chain.gz"
2024-04-05 16:10:50.221107: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.chain.gz" in 0.6143 seconds and 1.8 Mi memory
2024-04-05 16:10:50.221452: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.chain"
2024-04-05 16:10:54.872150: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.chain" in 4.65 seconds and 570.7 Mi memory
2024-04-05 16:10:54.872474: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:10:55.001279: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1282 seconds and 3.8 Mi memory
2024-04-05 16:10:55.001461: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 16:10:55.405380: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.bb" in 0.4034 seconds and 12.6 Mi memory
2024-04-05 16:10:55.405650: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:11:03.917345: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/bigLink.as -tab /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.link /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2.chrom.sizes /data/tmp/b734be1642a750a8912cb9c21ffd5921/856b/9006/tmpvnrejnjo/GCA_028885655.2_vs_GCA_028858775.2.bigChain.link.bb" in 21.7128 seconds and 142.6 Mi memory
2024-04-05 16:11:12.198946: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.7927 seconds and 8.0 Mi memory
2024-04-05 16:11:12.199178: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 16:11:33.855737: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/a470/e69b/tmpg_g3m5c1/GCA_028885655.2_vs_GCA_029289425.2.bigChain.link.bb" in 21.6558 seconds and 142.5 Mi memory
2024-04-05 16:11:50.942005: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/8-t2t-apes-2023v2.hal GCA_028858775.2 /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028858775.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028885625.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/30e9/tmpn98eqhrl/GCA_028858775.2.2bit /dev/stdout | gzip'" in 14115.9703 seconds and 24.6 Gi memory
2024-04-05 16:11:51.055944: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.chain.gz"
2024-04-05 16:11:51.685975: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.chain.gz" in 0.6291 seconds and 1.7 Mi memory
2024-04-05 16:11:51.686319: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.chain"
2024-04-05 16:11:56.670467: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.chain" in 4.9835 seconds and 561.4 Mi memory
2024-04-05 16:11:56.670817: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:11:56.850078: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1784 seconds and 3.8 Mi memory
2024-04-05 16:11:56.850314: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.bb"
2024-04-05 16:11:57.206015: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.bb" in 0.3549 seconds and 12.5 Mi memory
2024-04-05 16:11:57.206423: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:12:14.671752: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 17.4646 seconds and 8.0 Mi memory
2024-04-05 16:12:14.671990: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.link.bb"
2024-04-05 16:12:22.295381: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/8-t2t-apes-2023v2.hal hs1 /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/hs1.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/GCA_028885625.2.2bit /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/0c51/tmpy7zb5t46/hs1.2bit /dev/stdout | gzip'" in 14146.8499 seconds and 24.4 Gi memory
2024-04-05 16:12:22.509156: Running the command: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.chain.gz"
2024-04-05 16:12:23.127125: Successfully ran: "gzip -dc /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.chain.gz" in 0.617 seconds and 1.9 Mi memory
2024-04-05 16:12:23.127442: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.chain"
2024-04-05 16:12:28.002555: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.chain" in 4.8744 seconds and 556.8 Mi memory
2024-04-05 16:12:28.002857: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:12:28.111947: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1084 seconds and 3.7 Mi memory
2024-04-05 16:12:28.112166: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.bb"
2024-04-05 16:12:28.424781: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/bigChain.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.bb" in 0.3119 seconds and 11.1 Mi memory
2024-04-05 16:12:28.425111: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:12:35.020738: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/3ce3/826f/tmptep1uwc1/GCA_028885625.2_vs_GCA_028858775.2.bigChain.link.bb" in 20.348 seconds and 71.1 Mi memory
2024-04-05 16:12:45.421983: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 16.9961 seconds and 8.0 Mi memory
2024-04-05 16:12:45.422198: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.link.bb"
2024-04-05 16:13:07.087863: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/bigLink.as -tab /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.link /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2.chrom.sizes /data/tmp/dae98725ec685b99864fd6e197aa63da/6229/d9b1/tmp2ztfrv71/GCA_028885625.2_vs_hs1.bigChain.link.bb" in 21.6649 seconds and 140.9 Mi memory
2024-04-05 16:14:16.417591: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/GCA_028878055.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/12a0/tmpdt2ayml5/GCA_028878055.2.2bit /dev/stdout | gzip'" in 14255.8147 seconds and 21.6 Gi memory
2024-04-05 16:14:16.530956: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.chain.gz"
2024-04-05 16:14:17.224609: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.chain.gz" in 0.6927 seconds and 1.7 Mi memory
2024-04-05 16:14:17.224923: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.chain"
2024-04-05 16:14:22.559469: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.chain" in 5.3338 seconds and 594.8 Mi memory
2024-04-05 16:14:22.559787: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:14:22.666823: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1063 seconds and 3.8 Mi memory
2024-04-05 16:14:22.667040: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 16:14:22.973144: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.bb" in 0.3054 seconds and 10.9 Mi memory
2024-04-05 16:14:22.973472: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:14:37.198526: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/8-t2t-apes-2023v2.hal GCA_028878055.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/GCA_028878055.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/hg38.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/be15/tmpm8t3l_cm/GCA_028878055.2.2bit /dev/stdout | gzip'" in 14275.4728 seconds and 21.6 Gi memory
2024-04-05 16:14:37.280067: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.chain.gz"
2024-04-05 16:14:38.047607: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.chain.gz" in 0.7665 seconds and 1.8 Mi memory
2024-04-05 16:14:38.048028: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.chain"
2024-04-05 16:14:41.122613: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.1484 seconds and 7.9 Mi memory
2024-04-05 16:14:41.122819: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 16:14:43.925946: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.chain" in 5.8771 seconds and 610.6 Mi memory
2024-04-05 16:14:43.926336: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:14:44.035485: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1084 seconds and 3.8 Mi memory
2024-04-05 16:14:44.035749: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.bb"
2024-04-05 16:14:44.362734: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.bb" in 0.3263 seconds and 11.0 Mi memory
2024-04-05 16:14:44.363096: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:15:03.957117: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/5c91/4c0a/tmpnxtgsqj4/hs1_vs_GCA_028878055.2.bigChain.link.bb" in 22.8335 seconds and 83.5 Mi memory
2024-04-05 16:15:04.148350: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 19.7845 seconds and 7.9 Mi memory
2024-04-05 16:15:04.148629: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.link.bb"
2024-04-05 16:15:29.241070: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a060/09aa/tmpe7nbz0a8/hg38_vs_GCA_028878055.2.bigChain.link.bb" in 25.0916 seconds and 84.1 Mi memory
2024-04-05 16:17:13.778759: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/8-t2t-apes-2023v2.hal hs1 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/hs1.bed GCA_028878055.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/GCA_028878055.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/34b8/tmp_3rg0cni/hs1.2bit /dev/stdout | gzip'" in 14438.786 seconds and 22.4 Gi memory
2024-04-05 16:17:14.662972: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.chain.gz"
2024-04-05 16:17:15.826978: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.chain.gz" in 1.1627 seconds and 1.8 Mi memory
2024-04-05 16:17:15.827456: Running the command: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.chain"
2024-04-05 16:17:26.411546: Successfully ran: "hgLoadChain -noBin -test GCA_028878055.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.chain" in 10.583 seconds and 596.1 Mi memory
2024-04-05 16:17:26.411991: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:17:26.707508: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.2944 seconds and 3.8 Mi memory
2024-04-05 16:17:26.708081: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.bb"
2024-04-05 16:17:27.238801: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.bb" in 0.5296 seconds and 11.1 Mi memory
2024-04-05 16:17:27.239234: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:18:07.484858: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 40.2448 seconds and 8.0 Mi memory
2024-04-05 16:18:07.485206: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.link.bb"
2024-04-05 16:18:50.263987: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/823c/8b80/tmpj01z1nup/GCA_028878055.2_vs_hs1.bigChain.link.bb" in 42.7776 seconds and 66.8 Mi memory
2024-04-05 16:33:40.802674: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/8-t2t-apes-2023v2.hal GCA_029289425.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_029289425.2.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_028885625.2.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/4216/tmpl1v1l9f0/GCA_029289425.2.2bit /dev/stdout | gzip'" in 15421.3718 seconds and 24.5 Gi memory
2024-04-05 16:33:40.877195: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.chain.gz"
2024-04-05 16:33:41.563412: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.chain.gz" in 0.6852 seconds and 1.8 Mi memory
2024-04-05 16:33:41.563783: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.chain"
2024-04-05 16:33:46.797637: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.chain" in 5.233 seconds and 565.0 Mi memory
2024-04-05 16:33:46.798018: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:33:46.930701: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1319 seconds and 3.8 Mi memory
2024-04-05 16:33:46.930909: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.bb"
2024-04-05 16:33:47.311408: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.bb" in 0.3798 seconds and 11.3 Mi memory
2024-04-05 16:33:47.311760: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:34:06.407162: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 19.0947 seconds and 7.9 Mi memory
2024-04-05 16:34:06.407386: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.link.bb"
2024-04-05 16:34:30.563601: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/aa23/facf/tmpidma6sk4/GCA_028885625.2_vs_GCA_029289425.2.bigChain.link.bb" in 24.1554 seconds and 142.6 Mi memory
2024-04-05 16:38:29.225593: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028885655.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028858775.2.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/6a62/tmpjrl_ds09/GCA_028885655.2.2bit /dev/stdout | gzip'" in 15701.3518 seconds and 24.5 Gi memory
2024-04-05 16:38:29.295186: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.chain.gz"
2024-04-05 16:38:29.903178: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.chain.gz" in 0.6071 seconds and 1.7 Mi memory
2024-04-05 16:38:29.903551: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.chain"
2024-04-05 16:38:34.547875: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.chain" in 4.6436 seconds and 567.6 Mi memory
2024-04-05 16:38:34.548224: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:38:34.660525: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1116 seconds and 3.8 Mi memory
2024-04-05 16:38:34.660769: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 16:38:35.027427: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.bb" in 0.366 seconds and 12.3 Mi memory
2024-04-05 16:38:35.027786: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:38:52.224339: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 17.1958 seconds and 7.9 Mi memory
2024-04-05 16:38:52.224582: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 16:39:13.852165: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/ae10/db96/tmp75q77ci2/GCA_028858775.2_vs_GCA_028885655.2.bigChain.link.bb" in 21.6268 seconds and 143.1 Mi memory
2024-04-05 16:39:49.907535: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/8-t2t-apes-2023v2.hal hs1 /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/hs1.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/GCA_028885655.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/2664/tmpimb18zrr/hs1.2bit /dev/stdout | gzip'" in 15789.9639 seconds and 24.4 Gi memory
2024-04-05 16:39:49.998732: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.chain.gz"
2024-04-05 16:39:50.654206: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.chain.gz" in 0.6546 seconds and 1.9 Mi memory
2024-04-05 16:39:50.654525: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.chain"
2024-04-05 16:39:55.725340: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.chain" in 5.0701 seconds and 561.4 Mi memory
2024-04-05 16:39:55.725638: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 16:39:55.845063: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1187 seconds and 3.8 Mi memory
2024-04-05 16:39:55.845269: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.bb"
2024-04-05 16:39:56.188848: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.bb" in 0.3428 seconds and 11.3 Mi memory
2024-04-05 16:39:56.189188: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 16:40:14.504567: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.3146 seconds and 7.9 Mi memory
2024-04-05 16:40:14.504770: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.link.bb"
2024-04-05 16:40:37.989436: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/7550/413b/tmpa7_n0ihy/GCA_028885655.2_vs_hs1.bigChain.link.bb" in 23.4839 seconds and 141.1 Mi memory
9 jobs are running, 0 jobs are issued and waiting to run
2024-04-05 17:03:16.739997: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028885625.2.bed GCA_028858775.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028858775.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/0ce2/tmpwmth8451/GCA_028885625.2.2bit /dev/stdout | gzip'" in 17195.4232 seconds and 24.5 Gi memory
2024-04-05 17:03:16.815594: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.chain.gz"
2024-04-05 17:03:17.525138: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.chain.gz" in 0.7085 seconds and 1.8 Mi memory
2024-04-05 17:03:17.525542: Running the command: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.chain"
2024-04-05 17:03:22.913123: Successfully ran: "hgLoadChain -noBin -test GCA_028858775.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.chain" in 5.3867 seconds and 561.8 Mi memory
2024-04-05 17:03:22.913523: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:03:23.038677: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1243 seconds and 3.7 Mi memory
2024-04-05 17:03:23.038940: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 17:03:23.413502: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.bb" in 0.3737 seconds and 11.1 Mi memory
2024-04-05 17:03:23.413921: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:03:43.281813: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 19.8671 seconds and 8.0 Mi memory
2024-04-05 17:03:43.282068: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 17:04:06.409836: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/29fc/6d94/tmp8ccr8usd/GCA_028858775.2_vs_GCA_028885625.2.bigChain.link.bb" in 23.1269 seconds and 71.3 Mi memory
2024-04-05 17:04:36.508406: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_028885625.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_029289425.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/8ac6/tmpta7l2792/GCA_028885625.2.2bit /dev/stdout | gzip'" in 17275.0382 seconds and 24.5 Gi memory
2024-04-05 17:04:36.830873: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.chain.gz"
2024-04-05 17:04:37.537257: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.chain.gz" in 0.7053 seconds and 1.8 Mi memory
2024-04-05 17:04:37.537685: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.chain"
2024-04-05 17:04:42.921586: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.chain" in 5.383 seconds and 565.5 Mi memory
2024-04-05 17:04:42.921976: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:04:43.058729: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.136 seconds and 3.8 Mi memory
2024-04-05 17:04:43.058952: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 17:04:43.454675: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.bb" in 0.3951 seconds and 11.3 Mi memory
2024-04-05 17:04:43.454960: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:04:53.832570: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/GCA_028885655.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/hs1.2bit /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/fb0d/tmpjnd430sd/GCA_028885655.2.2bit /dev/stdout | gzip'" in 17284.6644 seconds and 24.1 Gi memory
2024-04-05 17:04:53.904641: Running the command: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.chain.gz"
2024-04-05 17:04:54.511656: Successfully ran: "gzip -dc /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.chain.gz" in 0.6061 seconds and 1.8 Mi memory
2024-04-05 17:04:54.511999: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.chain"
2024-04-05 17:04:59.126359: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.chain" in 4.6137 seconds and 563.0 Mi memory
2024-04-05 17:04:59.126703: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:04:59.247136: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1197 seconds and 3.8 Mi memory
2024-04-05 17:04:59.247341: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 17:04:59.596336: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/bigChain.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.bb" in 0.3484 seconds and 11.2 Mi memory
2024-04-05 17:04:59.596610: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:05:03.262986: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 19.8073 seconds and 7.9 Mi memory
2024-04-05 17:05:03.263251: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 17:05:06.500442: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_028885655.2.bed GCA_029289425.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_029289425.2.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/1640/tmpgph2o9wq/GCA_028885655.2.2bit /dev/stdout | gzip'" in 17305.8847 seconds and 24.5 Gi memory
2024-04-05 17:05:06.624102: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.chain.gz"
2024-04-05 17:05:07.280978: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.chain.gz" in 0.656 seconds and 1.9 Mi memory
2024-04-05 17:05:07.281296: Running the command: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.chain"
2024-04-05 17:05:12.279979: Successfully ran: "hgLoadChain -noBin -test GCA_029289425.2 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.chain" in 4.998 seconds and 571.4 Mi memory
2024-04-05 17:05:12.280265: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:05:12.411046: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1301 seconds and 3.8 Mi memory
2024-04-05 17:05:12.411245: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 17:05:12.834618: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.bb" in 0.4227 seconds and 12.5 Mi memory
2024-04-05 17:05:12.834962: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:05:15.108131: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 15.5108 seconds and 8.0 Mi memory
2024-04-05 17:05:15.108369: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 17:05:26.331771: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/ce7e/418e/tmptsr2r82z/GCA_029289425.2_vs_GCA_028885625.2.bigChain.link.bb" in 23.0677 seconds and 71.2 Mi memory
2024-04-05 17:05:31.066524: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 18.2309 seconds and 7.9 Mi memory
2024-04-05 17:05:31.066741: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 17:05:36.247927: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/bigLink.as -tab /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.link /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1.chrom.sizes /data/tmp/c4357560557a5660bebe2ad92e6556af/4eed/bce1/tmpmf8a7xjt/hs1_vs_GCA_028885655.2.bigChain.link.bb" in 21.1388 seconds and 134.6 Mi memory
2024-04-05 17:05:54.475277: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/a31f/c7f3/tmpnybe_i0j/GCA_029289425.2_vs_GCA_028885655.2.bigChain.link.bb" in 23.4078 seconds and 143.1 Mi memory
2024-04-05 17:07:12.766608: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/8-t2t-apes-2023v2.hal hg38 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/hg38.bed GCA_028885625.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/GCA_028885625.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/08a2/tmpzb0230rg/hg38.2bit /dev/stdout | gzip'" in 17437.8371 seconds and 24.4 Gi memory
2024-04-05 17:07:13.206976: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.chain.gz"
2024-04-05 17:07:14.296839: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.chain.gz" in 1.0846 seconds and 1.9 Mi memory
2024-04-05 17:07:14.297352: Running the command: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.chain"
2024-04-05 17:07:24.243511: Successfully ran: "hgLoadChain -noBin -test GCA_028885625.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.chain" in 9.945 seconds and 573.9 Mi memory
2024-04-05 17:07:24.244056: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:07:24.445859: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.2007 seconds and 3.7 Mi memory
2024-04-05 17:07:24.446164: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.bb"
2024-04-05 17:07:25.127936: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.bb" in 0.6808 seconds and 11.2 Mi memory
2024-04-05 17:07:25.128480: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:08:03.637075: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 38.5075 seconds and 8.0 Mi memory
2024-04-05 17:08:03.637624: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.link.bb"
2024-04-05 17:08:49.561120: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/b2bc/5084/tmprp1a8vrj/GCA_028885625.2_vs_hg38.bigChain.link.bb" in 45.9224 seconds and 140.8 Mi memory
2024-04-05 17:18:22.838244: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/8-t2t-apes-2023v2.hal hg38 /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/hg38.bed GCA_028885655.2 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/GCA_028885655.2.2bit /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/041e/tmp4csr1fok/hg38.2bit /dev/stdout | gzip'" in 18109.49 seconds and 24.4 Gi memory
2024-04-05 17:18:23.463038: Running the command: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.chain.gz"
2024-04-05 17:18:24.585360: Successfully ran: "gzip -dc /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.chain.gz" in 1.121 seconds and 1.8 Mi memory
2024-04-05 17:18:24.585855: Running the command: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.chain"
2024-04-05 17:18:35.643561: Successfully ran: "hgLoadChain -noBin -test GCA_028885655.2 bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.chain" in 11.0566 seconds and 577.2 Mi memory
2024-04-05 17:18:35.644098: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:18:35.996138: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.3501 seconds and 3.7 Mi memory
2024-04-05 17:18:35.996487: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.bb"
2024-04-05 17:18:36.784490: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/bigChain.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.bb" in 0.7869 seconds and 11.3 Mi memory
2024-04-05 17:18:36.785009: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:19:15.987802: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 39.2017 seconds and 8.0 Mi memory
2024-04-05 17:19:15.988135: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.link.bb"
2024-04-05 17:20:01.150341: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/bigLink.as -tab /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.link /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2.chrom.sizes /data/tmp/d5dea97b34ab588c9e17b054b4c00bcb/9e37/15e8/tmp588bf2r9/GCA_028885655.2_vs_hg38.bigChain.link.bb" in 45.1611 seconds and 141.0 Mi memory
2024-04-05 17:38:27.275008: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/GCA_028885625.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/hg38.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/db22/tmpsg1698ay/GCA_028885625.2.2bit /dev/stdout | gzip'" in 19306.8749 seconds and 24.1 Gi memory
2024-04-05 17:38:27.352374: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.chain.gz"
2024-04-05 17:38:28.050702: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.chain.gz" in 0.6974 seconds and 1.8 Mi memory
2024-04-05 17:38:28.051114: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.chain"
2024-04-05 17:38:33.318587: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.chain" in 5.2668 seconds and 576.1 Mi memory
2024-04-05 17:38:33.318926: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:38:33.473093: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1534 seconds and 3.7 Mi memory
2024-04-05 17:38:33.473332: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 17:38:33.928775: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.bb" in 0.4547 seconds and 11.7 Mi memory
2024-04-05 17:38:33.929132: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:38:51.724635: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 17.7948 seconds and 7.9 Mi memory
2024-04-05 17:38:51.724901: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 17:39:15.692692: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/1be0/a15f/tmp_hu8ek63/hg38_vs_GCA_028885625.2.bigChain.link.bb" in 23.9669 seconds and 136.7 Mi memory
2024-04-05 17:42:02.055836: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/8-t2t-apes-2023v2.hal GCA_028885625.2 /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/GCA_028885625.2.bed hs1 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/hs1.2bit /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/7243/tmp1l4cyap_/GCA_028885625.2.2bit /dev/stdout | gzip'" in 19521.9248 seconds and 24.1 Gi memory
2024-04-05 17:42:05.354064: Running the command: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.chain.gz"
2024-04-05 17:42:06.276145: Successfully ran: "gzip -dc /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.chain.gz" in 0.9206 seconds and 1.9 Mi memory
2024-04-05 17:42:06.276548: Running the command: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.chain"
2024-04-05 17:42:14.241657: Successfully ran: "hgLoadChain -noBin -test hs1 bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.chain" in 7.9641 seconds and 558.3 Mi memory
2024-04-05 17:42:14.242068: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:42:14.407828: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1649 seconds and 3.7 Mi memory
2024-04-05 17:42:14.408061: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.bb"
2024-04-05 17:42:14.985801: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/bigChain.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.bb" in 0.577 seconds and 11.3 Mi memory
2024-04-05 17:42:14.986257: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:42:40.449976: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 25.4627 seconds and 8.0 Mi memory
2024-04-05 17:42:40.450214: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.link.bb"
2024-04-05 17:43:14.877735: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/bigLink.as -tab /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.link /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1.chrom.sizes /data/tmp/626241477d305938ad450ad4a7dbf27d/2492/3c4f/tmp78vcmk16/hs1_vs_GCA_028885625.2.bigChain.link.bb" in 34.4267 seconds and 134.4 Mi memory
2024-04-05 17:44:51.854849: Successfully ran: "bash -c 'set -eo pipefail && halLiftover /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/8-t2t-apes-2023v2.hal GCA_028885655.2 /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/GCA_028885655.2.bed hg38 /dev/stdout --outPSL --inMemory | pslPosTarget /dev/stdin /dev/stdout | axtChain -psl -verbose=0 -linearGap=medium /dev/stdin /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/hg38.2bit /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/c581/tmp70th5564/GCA_028885655.2.2bit /dev/stdout | gzip'" in 19691.591 seconds and 24.1 Gi memory
2024-04-05 17:44:52.443734: Running the command: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.chain.gz"
2024-04-05 17:44:53.131181: Successfully ran: "gzip -dc /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.chain.gz" in 0.6861 seconds and 1.9 Mi memory
2024-04-05 17:44:53.131538: Running the command: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.chain"
2024-04-05 17:44:58.350907: Successfully ran: "hgLoadChain -noBin -test hg38 bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.chain" in 5.2185 seconds and 580.0 Mi memory
2024-04-05 17:44:58.351252: Running the command: "bash -c set -eo pipefail && sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"
2024-04-05 17:44:58.506288: Successfully ran: "bash -c 'set -eo pipefail && sed '"'"'s/\.000000//'"'"' chain.tab | awk '"'"'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}'"'"''" in 0.1543 seconds and 3.7 Mi memory
2024-04-05 17:44:58.506509: Running the command: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.bb"
2024-04-05 17:44:58.963401: Successfully ran: "bedToBigBed -type=bed6+6 -as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/bigChain.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.bb" in 0.4562 seconds and 11.8 Mi memory
2024-04-05 17:44:58.963768: Running the command: "bash -c set -eo pipefail && awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n"
2024-04-05 17:45:16.430046: Successfully ran: "bash -c 'set -eo pipefail && awk '"'"'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}'"'"' link.tab | sort -k1,1 -k2,2n'" in 17.4656 seconds and 7.9 Mi memory
2024-04-05 17:45:16.430276: Running the command: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.link.bb"
2024-04-05 17:45:40.220395: Successfully ran: "bedToBigBed -type=bed4+1 as=/data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/bigLink.as -tab /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.link /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38.chrom.sizes /data/tmp/1a8f440a99865036b92cf438ab8edad9/999e/df9a/tmpjeg8kxa6/hg38_vs_GCA_028885655.2.bigChain.link.bb" in 23.7892 seconds and 136.8 Mi memory
Finished toil run successfully.
Stopping real-time logging server.
Joining real-time logging server thread.
Successfully deleted the job store: FileJobStore(/private/groups/cgl/hickey/work/t2t-apes-release-2/js_chains8)
cactus-hal2chains has finished after 20856.28098723502 seconds