/venv/bin/toil-vg map aws:us-west-2:glennhickey-jobstore HG002 s3://cgl-pipeline-inputs/vg_cgl/CHR21_DEC3/snp1kg-CHR21_DEC3.xg s3://glennhickey/outstore/chr21-dec-11-stage/chr21_Dec_3.gcsa aws:us-west-2:glennhickey/outstore/chr21-dec-11-stage/gam --gam_input_reads s3://glennhickey/mike-hs37d5-hg002-nov18/vg.pan/gams/snp1kg_HG002_21.proper.pair.gam --interleaved --whole_genome_config --batchSystem=mesos --mesosMaster=172.31.28.169:5050 --nodeTypes r3.8xlarge:0.85 --provisioner aws --realTimeLogging --logInfo --maxNodes 3 --logFile map.21.log --retryCount 3 --defaultPreemptable --single_reads_chunk

2017-12-15 14:33:07.311043
toil-vg version 1.3.1a1
Configuration:
chunk_context: 50
maxMemory: None
bam_input_reads: None
alignment_cores: 32
call_chunk_disk: 100G
rtg_docker: realtimegenomics/rtg-tools:3.8.4
multipath: False
mpmap_opts: ['-S']
disableCaching: False
prune_cores: 2
environment: []
vcfeval_disk: 64G
sample_name: HG002
augment_opts: ['-q', '10', '-a', 'pileup']
realTimeLogging: True
sseKey: None
defaultCores: None
sim_cores: 2
map_opts: []
interleaved: True
xg_index: s3://cgl-pipeline-inputs/vg_cgl/CHR21_DEC3/snp1kg-CHR21_DEC3.xg
readGlobalFileMutableByDefault: None
filter_opts: ['-r', '0.9', '-fu', '-s', '1000', '-m', '1', '-q', '15', '-D', '999']
freebayes_docker: maxulysse/freebayes:1.2.5
construct_disk: 32G
kmers_opts: ['-g', '-B', '-k', '16', '-H', '1000000000', '-T', '1000000001']
call_chunk_cores: 8
vcfeval_opts: []
logRotating: False
bwa_docker: quay.io/ucsc_cgl/bwa:latest
disableHotDeployment: None
linkImports: False
maxPreemptableServiceJobs: None
prune_disk: 60G
workDir: None
container: Docker
vg_docker: quay.io/vgteam/vg:v1.5.0-2018-g71f96239-t119-run
gcsa_opts: ['-X', '3', '-Z', '3000']
tabix_docker: vandhanak/bcftools:1.3.1
overlap: 5000
gcsa_index: s3://glennhickey/outstore/chr21-dec-11-stage/chr21_Dec_3.gcsa
bcftools_docker: vandhanak/bcftools:1.3.1
gam_input_reads: s3://glennhickey/mike-hs37d5-hg002-nov18/vg.pan/gams/snp1kg_HG002_21.proper.pair.gam
vcfeval_cores: 32
genotype_opts: []
maxServiceJobs: None
writeLogs: None
betaInertia: None
reads_per_chunk: 50000000
fq_split_disk: 200G
deadlockWait: None
parasolCommand: None
vcflib_docker: quay.io/biocontainers/vcflib:1.0.0_rc1--0
badWorkerFailInterval: None
defaultMemory: None
kmer_size: None
xg_index_disk: 200G
call_opts: []
logFile: map.21.log
samtools_docker: quay.io/ucsc_cgl/samtools:latest
logLevel: INFO
bwa_opts: []
jobStore: aws:us-west-2:glennhickey-jobstore
gcsa_index_cores: 32
id_ranges: None
nodeOptions: None
nodeTypes: r3.8xlarge:0.85
servicePollingInterval: None
calling_mem: 8G
genotype: False
writeLogsGzip: None
vcfeval_mem: 64G
minNodes: None
kmers_mem: 70G
maxDisk: None
cleanWorkDir: always
single_reads_chunk: True
alignment_mem: 100G
clusterStats: None
prune_opts: [['-D'], ['-p', '-l', '16', '-S', '-e', '4'], ['-S', '-l', '32']]
cseKey: None
jq_docker: devorbitus/ubuntu-bash-jq-curl
calling_cores: 1
maxNodes: 3
gcsa_index_mem: 200G
badWorker: None
mesosMasterAddress: 172.31.28.169:5050
preemptableCompensation: None
fq_split_cores: 32
whole_genome_config: True
alphaPacking: None
maxLogFileSize: None
force_outstore: False
r_docker: rocker/tidyverse:latest
construct_mem: 32G
maxJobDuration: None
out_store: aws:us-west-2:glennhickey/outstore/chr21-dec-11-stage/gam
call_chunk_mem: 100G
nodeStorage: 50
misc_mem: 1G
rescueJobsFrequency: None
pigz_docker: quay.io/glennhickey/pigz:latest
fastq: None
index_name: genome
defaultPreemptable: True
calling_disk: 8G
sim_disk: 200G
prune_mem: 60G
sim_mem: 60G
restart: None
parasolMaxBatches: None
misc_cores: 1
maxCores: None
config: None
kmers_disk: 60G
misc_disk: 1G
scaleInterval: None
alignment_disk: 100G
batchSystem: mesos
scale: None
fq_split_mem: 4G
retryCount: 3
xg_index_mem: 200G
stats: None
defaultDisk: None
call_chunk_size: 2000000
gcsa_index_disk: 3000G
statePollingWait: 1
construct_cores: 1
command: map
kmers_cores: 16
clean: None
provisioner: aws
xg_index_cores: 1
sim_opts: ['-l', '150', '-p', '500', '-v', '50', '-e', '0.01', '-i', '0.002']
gam_index_cores: 6