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dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
102 stars 39 forks source link

SSVIZ problem, job is taking too long #72

Closed jputerova closed 5 years ago

jputerova commented 5 years ago 
"prefix": "parliament2Tumor",
"filter_short_contigs": true,
"run_breakdancer": true,
"run_breakseq": true,
"run_manta": true,
"run_cnvnator": true,
"run_lumpy": true,
"run_delly_deletion": true,
"run_delly_insertion": true,
"run_delly_inversion": true,
"run_delly_duplication": true,
"run_genotype_candidates": true,
"run_svviz": true,
"svviz_only_validated_candidates": true,
"output_log_files": true

}

View log of failed sub-job

Logging initialized (priority) CPU: 7% (8 cores) Memory: 304/67740MB Storage: 1679GB free Net: 0↓/0↑MBps dxpy/0.282.0 (Linux-4.4.0-1084-aws-x86_64-with-Ubuntu-16.04-xenial) Setting SSH public key dxpy/0.282.0 (Linux-4.4.0-1084-aws-x86_64-with-Ubuntu-16.04-xenial) /usr/sbin/rsyslogd already running. /usr/sbin/sshd already running. Invoking main with {u'run_svviz': True, u'svviz_only_validated_candidates': True, u'filter_short_contigs': True, u'ref_fasta': {u'$dnanexus_link': u'file-B6qq93v2J35fB53gZ5G0007K'}, u'run_delly_duplication': True, u'run_delly_insertion': True, u'run_delly_deletion': True, u'output_log_files': True, u'prefix': u'parliament2Tumor', u'run_cnvnator': True, u'run_breakdancer': True, u'illumina_bai': {u'$dnanexus_link': u'file-FZ3vVv004B4FJ7V84B91kq8g'}, u'run_delly_inversion': True, u'illumina_bam': {u'$dnanexus_link': u'file-FZ3vVv004B40gXVK24z8Fq0J'}, u'ref_index': {u'$dnanexus_link': u'file-ByGVY5j04Y0xPfZZfQ0Y85p6'}, u'run_breakseq': True, u'run_lumpy': True, u'run_manta': True, u'run_genotype_candidates': True} 0.1.10: Pulling from dnanexus/parliament2 99ad4e3ced4d: Pulling fs layer ec5a723f4e2a: Pulling fs layer 2a175e11567c: Pulling fs layer 8d26426e95e0: Pulling fs layer 46e451596b7c: Pulling fs layer 7a2556f4d4d5: Pulling fs layer 701e9f1f0e38: Pulling fs layer 54ad0e44d750: Pulling fs layer b668c49313ee: Pulling fs layer 9408994aa68f: Pulling fs layer 3aa1a8390ff4: Pulling fs layer 42b5ae245a59: Pulling fs layer a9579715f5b2: Pulling fs layer 20562123dc36: Pulling fs layer 0cd94a37c156: Pulling fs layer 620ff9f6303f: Pulling fs layer df9f624c4106: Pulling fs layer 756c0e8d5ed8: Pulling fs layer 701e9f1f0e38: Waiting f5766963859f: Pulling fs layer 924323f643ca: Pulling fs layer 5556afd3b0d4: Pulling fs layer 0d29de6ac172: Pulling fs layer 54ad0e44d750: Waiting 8108a78f4edb: Pulling fs layer 558438e9ce84: Pulling fs layer b668c49313ee: Waiting 27e5b9d77fe8: Pulling fs layer 40bbf2a66780: Pulling fs layer 36d081368317: Pulling fs layer b67cdf7784ed: Pulling fs layer 3aa1a8390ff4: Waiting 1f5eeb181515: Pulling fs layer 15d196679ac0: Pulling fs layer 40ebfb8fe057: Pulling fs layer 42b5ae245a59: Waiting a9579715f5b2: Waiting ee018bb915b6: Pulling fs layer 487b27af9bba: Pulling fs layer 20562123dc36: Waiting ed7fada48184: Pulling fs layer 1b8a5a725147: Pulling 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'-r', '/home/dnanexus/in/ucsc_hg19.fa.gz', '--prefix', 'parliament2Tumor', '--bai', '/home/dnanexus/in/SP1TUnxWES_S2_L00.bam.bai', '--fai', '/home/dnanexus/in/ucsc_hg19.fa.fai', '--filter_short_contigs', '--breakdancer', '--breakseq', '--manta', '--cnvnator', '--lumpy', '--delly_inversion', '--delly_insertion', '--delly_deletion', '--delly_duplication', '--genotype', '--svviz', '--svviz_only_validated_candidates'] Set up and index BAM/CRAM BAM file input, index exists Generate contigs Launching jobs that cannot be parallelized by contig BreakSeq Manta Processing bam input.bam First read: 0 0 Launching jobs parallelized by contig Running on contig chr1 Running Breakdancer for contig chr1 Running CNVnator for contig chr1 Running sambamba view Read group SP1TUnxWES_S2_L004_001_1: ignoring insert sizes above 394 Read group SP1TUnxWES_S2_L003_001_1: ignoring insert sizes above 384 Read group SP1TUnxWES_S2_L002_001_1: ignoring insert sizes above 394 Read group SP1TUnxWES_S2_L001_001_1: ignoring insert sizes above 393 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 CPU: 55% (8 cores) Memory: 19580/67740MB Storage: 1645GB free Net: 2↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr1 Running Delly (inversions) for contig chr1 Running Delly (duplications) for contig chr1 Running Delly (insertions) for contig chr1 Running Lumpy for contig chr1 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr2 Running Breakdancer for contig chr2 Running CNVnator for contig chr2 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr2 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds CPU: 87% (8 cores) Memory: 21518/67740MB Storage: 1643GB free Net: 0↓/0↑MBps Running Delly (inversions) for contig chr2 Running Delly (duplications) for contig chr2 Running Delly (insertions) for contig chr2 Running Lumpy for contig chr2 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr3 Running Breakdancer for contig chr3 Running CNVnator for contig chr3 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr3 Running Delly (inversions) for contig chr3 Running Delly (duplications) for contig chr3 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds CPU: 82% (8 cores) Memory: 22499/67740MB Storage: 1642GB free Net: 0↓/0↑MBps Waiting for 60 seconds Running Delly (insertions) for contig chr3 Running Lumpy for contig chr3 Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr4 Running Breakdancer for contig chr4 Running CNVnator for contig chr4 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr4 Running Delly (inversions) for contig chr4 Running Delly (duplications) for contig chr4 Running Delly (insertions) for contig chr4 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr4 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr5 Running Breakdancer for contig chr5 Running CNVnator for contig chr5 Running sambamba view CPU: 74% (8 cores) Memory: 25725/67740MB Storage: 1641GB free Net: 0↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr5 Running Delly (inversions) for contig chr5 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr5 Running Delly (insertions) for contig chr5 Running Lumpy for contig chr5 Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6 Running Breakdancer for contig chr6 Running CNVnator for contig chr6 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6 Running Delly (inversions) for contig chr6 Running Delly (duplications) for contig chr6 Running Delly (insertions) for contig chr6 Waiting for 60 seconds Waiting for 60 seconds CPU: 81% (8 cores) Memory: 26607/67740MB Storage: 1639GB free Net: 0↓/0↑MBps Waiting for 60 seconds Running Lumpy for contig chr6 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr7 Running Breakdancer for contig chr7 Running CNVnator for contig chr7 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr7 Running Delly (inversions) for contig chr7 Running Delly (duplications) for contig chr7 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr7 Running Lumpy for contig chr7 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr8 Running Breakdancer for contig chr8 Running CNVnator for contig chr8 Waiting for 60 seconds Waiting for 60 seconds Running sambamba view CPU: 84% (8 cores) Memory: 28830/67740MB Storage: 1637GB free Net: 0↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr8 Running Delly (inversions) for contig chr8 Running Delly (duplications) for contig chr8 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr8 Running Lumpy for contig chr8 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr9 Running Breakdancer for contig chr9 Running CNVnator for contig chr9 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr9 Running Delly (inversions) for contig chr9 Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr9 Running Delly (insertions) for contig chr9 Waiting for 60 seconds Waiting for 60 seconds CPU: 83% (8 cores) Memory: 29918/67740MB Storage: 1635GB free Net: 0↓/0↑MBps Running Lumpy for contig chr9 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr10 Running Breakdancer for contig chr10 Running CNVnator for contig chr10 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr10 Running Delly (inversions) for contig chr10 Running Delly (duplications) for contig chr10 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr10 Running Lumpy for contig chr10 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr11 Running Breakdancer for contig chr11 Running CNVnator for contig chr11 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr11 Running Delly (inversions) for contig chr11 Waiting for 60 seconds Waiting for 60 seconds CPU: 79% (8 cores) Memory: 32457/67740MB Storage: 1633GB free Net: 0↓/0↑MBps Running Delly (duplications) for contig chr11 Running Delly (insertions) for contig chr11 Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr11 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr12 Running Breakdancer for contig chr12 Running CNVnator for contig chr12 Waiting for 60 seconds Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chr12 Running Delly (inversions) for contig chr12 Running Delly (duplications) for contig chr12 Running Delly (insertions) for contig chr12 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr12 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr13 Running Breakdancer for contig chr13 Running CNVnator for contig chr13 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr13 CPU: 79% (8 cores) Memory: 33673/67740MB Storage: 1632GB free Net: 0↓/0↑MBps Running Delly (inversions) for contig chr13 Running Delly (duplications) for contig chr13 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr13 Running Lumpy for contig chr13 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr14 Running Breakdancer for contig chr14 Running CNVnator for contig chr14 Waiting for 60 seconds Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chr14 Running Delly (inversions) for contig chr14 Running Delly (duplications) for contig chr14 Waiting for 60 seconds Running Delly (insertions) for contig chr14 Running Lumpy for contig chr14 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr15 Running Breakdancer for contig chr15 Running CNVnator for contig chr15 Waiting for 60 seconds Waiting for 60 seconds Running sambamba view CPU: 81% (8 cores) Memory: 35342/67740MB Storage: 1630GB free Net: 0↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr15 Running Delly (inversions) for contig chr15 Running Delly (duplications) for contig chr15 Running Delly (insertions) for contig chr15 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr15 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr16 Running Breakdancer for contig chr16 Running CNVnator for contig chr16 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr16 Running Delly (inversions) for contig chr16 Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr16 Running Delly (insertions) for contig chr16 Waiting for 60 seconds Waiting for 60 seconds CPU: 71% (8 cores) Memory: 35560/67740MB Storage: 1629GB free Net: 0↓/0↑MBps Running Lumpy for contig chr16 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr17 Running Breakdancer for contig chr17 Running CNVnator for contig chr17 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr17 Running Delly (inversions) for contig chr17 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr17 Running Delly (insertions) for contig chr17 Running Lumpy for contig chr17 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr18 Running Breakdancer for contig chr18 Running CNVnator for contig chr18 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chr18 Running Delly (inversions) for contig chr18 Waiting for 60 seconds CPU: 70% (8 cores) Memory: 37906/67740MB Storage: 1627GB free Net: 0↓/0↑MBps Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr18 Running Delly (insertions) for contig chr18 Running Lumpy for contig chr18 Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr19 Running Breakdancer for contig chr19 Running CNVnator for contig chr19 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr19 Running Delly (inversions) for contig chr19 Running Delly (duplications) for contig chr19 Running Delly (insertions) for contig chr19 Waiting for 60 seconds Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr19 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr20 Running Breakdancer for contig chr20 Running CNVnator for contig chr20 Running sambamba view CPU: 63% (8 cores) Memory: 38666/67740MB Storage: 1626GB free Net: 0↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr20 Running Delly (inversions) for contig chr20 Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr20 Running Delly (insertions) for contig chr20 Running Lumpy for contig chr20 Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr21 Running Breakdancer for contig chr21 Running CNVnator for contig chr21 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr21 Running Delly (inversions) for contig chr21 Running Delly (duplications) for contig chr21 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr21 Running Lumpy for contig chr21 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr22 Running Breakdancer for contig chr22 Running CNVnator for contig chr22 Waiting for 60 seconds Waiting for 60 seconds Running sambamba view CPU: 64% (8 cores) Memory: 40694/67740MB Storage: 1625GB free Net: 0↓/0↑MBps Running sambamba index Running Delly (deletions) for contig chr22 Running Delly (inversions) for contig chr22 Running Delly (duplications) for contig chr22 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr22 Running Lumpy for contig chr22 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chrX Running Breakdancer for contig chrX Running CNVnator for contig chrX Waiting for 60 seconds Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chrX Running Delly (inversions) for contig chrX Running Delly (duplications) for contig chrX Running Delly (insertions) for contig chrX Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chrX samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chrY Running Breakdancer for contig chrY Running CNVnator for contig chrY Running sambamba view Running sambamba index Running Delly (deletions) for contig chrY Running Delly (inversions) for contig chrY Waiting for 60 seconds Waiting for 60 seconds CPU: 71% (8 cores) Memory: 41561/67740MB Storage: 1624GB free Net: 0↓/0↑MBps Running Delly (duplications) for contig chrY Running Delly (insertions) for contig chrY Running Lumpy for contig chrY Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_apd_hap1 Running Breakdancer for contig chr6_apd_hap1 Running CNVnator for contig chr6_apd_hap1 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_apd_hap1 Waiting for 60 seconds Waiting for 60 seconds Running Delly (inversions) for contig chr6_apd_hap1 Running Delly (duplications) for contig chr6_apd_hap1 Running Delly (insertions) for contig chr6_apd_hap1 Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr6_apd_hap1 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_cox_hap2 Running Breakdancer for contig chr6_cox_hap2 Running CNVnator for contig chr6_cox_hap2 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_cox_hap2 Running Delly (inversions) for contig chr6_cox_hap2 Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr6_cox_hap2 Running Delly (insertions) for contig chr6_cox_hap2 Running Lumpy for contig chr6_cox_hap2 Waiting for 60 seconds CPU: 60% (8 cores) Memory: 41860/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_dbb_hap3 Running Breakdancer for contig chr6_dbb_hap3 Running CNVnator for contig chr6_dbb_hap3 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_dbb_hap3 Running Delly (inversions) for contig chr6_dbb_hap3 Waiting for 60 seconds Waiting for 60 seconds Running Delly (duplications) for contig chr6_dbb_hap3 Running Delly (insertions) for contig chr6_dbb_hap3 Running Lumpy for contig chr6_dbb_hap3 Waiting for 60 seconds Waiting for 60 seconds samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_mann_hap4 Running Breakdancer for contig chr6_mann_hap4 Running CNVnator for contig chr6_mann_hap4 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_mann_hap4 Running Delly (inversions) for contig chr6_mann_hap4 Running Delly (duplications) for contig chr6_mann_hap4 Running Delly (insertions) for contig chr6_mann_hap4 Waiting for 60 seconds Waiting for 60 seconds Running Lumpy for contig chr6_mann_hap4 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_mcf_hap5 Running Breakdancer for contig chr6_mcf_hap5 Running CNVnator for contig chr6_mcf_hap5 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_mcf_hap5 Running Delly (inversions) for contig chr6_mcf_hap5 Running Delly (duplications) for contig chr6_mcf_hap5 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr6_mcf_hap5 CPU: 48% (8 cores) Memory: 42174/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Running Lumpy for contig chr6_mcf_hap5 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_qbl_hap6 Running Breakdancer for contig chr6_qbl_hap6 Running CNVnator for contig chr6_qbl_hap6 Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_qbl_hap6 Running Delly (inversions) for contig chr6_qbl_hap6 Running Delly (duplications) for contig chr6_qbl_hap6 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr6_qbl_hap6 Running Lumpy for contig chr6_qbl_hap6 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6_ssto_hap7 Running Breakdancer for contig chr6_ssto_hap7 Running CNVnator for contig chr6_ssto_hap7 Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chr6_ssto_hap7 Running Delly (inversions) for contig chr6_ssto_hap7 Running Delly (duplications) for contig chr6_ssto_hap7 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr6_ssto_hap7 Running Lumpy for contig chr6_ssto_hap7 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr17_ctg5_hap1 Running Breakdancer for contig chr17_ctg5_hap1 Running CNVnator for contig chr17_ctg5_hap1 Waiting for 60 seconds Running sambamba view Running sambamba index Running Delly (deletions) for contig chr17_ctg5_hap1 Running Delly (inversions) for contig chr17_ctg5_hap1 Running Delly (duplications) for contig chr17_ctg5_hap1 Waiting for 60 seconds Waiting for 60 seconds Running Delly (insertions) for contig chr17_ctg5_hap1 Running Lumpy for contig chr17_ctg5_hap1 CPU: 57% (8 cores) Memory: 42097/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Converting results to VCF format Convert Lumpy results to VCF format Convert Manta results to VCF format Convert Breakdancer results to VCF format Convert CNVnator results to VCF format 16K 1.delly.deletion.vcf 16K 1.delly.duplication.vcf 8.0K 1.delly.insertion.vcf 16K 1.delly.inversion.vcf 12K 10.delly.deletion.vcf 12K 10.delly.duplication.vcf 4.0K 10.delly.insertion.vcf 8.0K 10.delly.inversion.vcf 8.0K 11.delly.deletion.vcf 12K 11.delly.duplication.vcf 4.0K 11.delly.insertion.vcf 8.0K 11.delly.inversion.vcf 12K 12.delly.deletion.vcf 12K 12.delly.duplication.vcf 4.0K 12.delly.insertion.vcf 8.0K 12.delly.inversion.vcf 8.0K 13.delly.deletion.vcf 8.0K 13.delly.duplication.vcf 4.0K 13.delly.inversion.vcf 12K 14.delly.deletion.vcf 8.0K 14.delly.duplication.vcf 4.0K 14.delly.insertion.vcf 8.0K 14.delly.inversion.vcf 8.0K 15.delly.deletion.vcf 8.0K 15.delly.duplication.vcf 8.0K 15.delly.inversion.vcf 8.0K 16.delly.deletion.vcf 8.0K 16.delly.duplication.vcf 4.0K 16.delly.insertion.vcf 8.0K 16.delly.inversion.vcf 8.0K 17.delly.deletion.vcf 12K 17.delly.duplication.vcf 8.0K 17.delly.inversion.vcf 8.0K 18.delly.deletion.vcf 8.0K 18.delly.duplication.vcf 4.0K 18.delly.insertion.vcf 8.0K 18.delly.inversion.vcf 8.0K 19.delly.deletion.vcf 8.0K 19.delly.duplication.vcf 4.0K 19.delly.insertion.vcf 8.0K 19.delly.inversion.vcf 64K 2.delly.deletion.vcf 16K 2.delly.duplication.vcf 4.0K 2.delly.insertion.vcf 288K 2.delly.inversion.vcf 8.0K 20.delly.deletion.vcf 8.0K 20.delly.duplication.vcf 8.0K 20.delly.inversion.vcf 4.0K 21.delly.deletion.vcf 4.0K 21.delly.duplication.vcf 8.0K 21.delly.inversion.vcf 8.0K 22.delly.deletion.vcf 8.0K 22.delly.duplication.vcf 8.0K 22.delly.inversion.vcf 4.0K 23.delly.deletion.vcf 4.0K 23.delly.duplication.vcf 4.0K 23.delly.inversion.vcf 8.0K 24.delly.deletion.vcf 8.0K 24.delly.duplication.vcf 4.0K 24.delly.inversion.vcf 12K 3.delly.deletion.vcf 12K 3.delly.duplication.vcf 4.0K 3.delly.insertion.vcf 8.0K 3.delly.inversion.vcf 8.0K 4.delly.deletion.vcf 12K 4.delly.duplication.vcf 4.0K 4.delly.insertion.vcf 8.0K 4.delly.inversion.vcf 8.0K 5.delly.deletion.vcf 8.0K 5.delly.duplication.vcf 4.0K 5.delly.insertion.vcf 8.0K 5.delly.inversion.vcf 8.0K 6.delly.deletion.vcf 8.0K 6.delly.duplication.vcf 4.0K 6.delly.insertion.vcf 8.0K 6.delly.inversion.vcf 12K 7.delly.deletion.vcf 12K 7.delly.duplication.vcf 4.0K 7.delly.insertion.vcf 12K 7.delly.inversion.vcf 12K 8.delly.deletion.vcf 8.0K 8.delly.duplication.vcf 4.0K 8.delly.insertion.vcf 8.0K 8.delly.inversion.vcf 8.0K 9.delly.deletion.vcf 8.0K 9.delly.duplication.vcf 4.0K 9.delly.insertion.vcf 8.0K 9.delly.inversion.vcf 4.0K lumpy.23.vcf 4.0K lumpy.27.vcf 4.0K lumpy.32.vcf Convert Delly deletion results to VCF format Convert Breakseq results to VCF format No outputs of Breakseq found. Continuing. Convert Delly inversion results to VCF format Convert Delly duplication results to VCF format Convert Delly insertion results to VCF format No Breakseq log files found. Reading calls ... Can't parse sequence for chromosome chr1. Can't parse sequence for chromosome chr2. Can't parse sequence for chromosome chr3. Can't parse sequence for chromosome chr4. Can't parse sequence for chromosome chr5. Can't parse sequence for chromosome chr6. Can't parse sequence for chromosome chr7. Can't parse sequence for chromosome chr8. Can't parse sequence for chromosome chr9. Can't parse sequence for chromosome chr10. Can't parse sequence for chromosome chr11. Can't parse sequence for chromosome chr12. Can't parse sequence for chromosome chr13. Can't parse sequence for chromosome chr14. Can't parse sequence for chromosome chr15. Can't parse sequence for chromosome chr16. Can't parse sequence for chromosome chr17. Can't parse sequence for chromosome chr18. Can't parse sequence for chromosome chr19. Can't parse sequence for chromosome chr20. Can't parse sequence for chromosome chr21. Can't parse sequence for chromosome chr22. Can't parse sequence for chromosome chrX. Can't parse sequence for chromosome chrY. Can't parse sequence for chromosome chr6_apd_hap1. Can't parse sequence for chromosome chr6_cox_hap2. Can't parse sequence for chromosome chr6_dbb_hap3. Can't parse sequence for chromosome chr6_mann_hap4. Can't parse sequence for chromosome chr6_mcf_hap5. Can't parse sequence for chromosome chr6_qbl_hap6. Can't parse sequence for chromosome chr6_ssto_hap7. Can't parse sequence for chromosome chr17_ctg5_hap1. Running SVTyper Running SVTyper on Breakdancer outputs grep: svtype_breakdancer: Is a directory CPU: 40% (8 cores) Memory: 40012/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 99% (8 cores) Memory: 39976/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 98% (8 cores) Memory: 39956/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Running SVTyper on BreakSeq outputs No BreakSeq VCF file found. Continuing. Running SVTyper on CNVnator outputs grep: svtype_cnvnator: Is a directory CPU: 92% (8 cores) Memory: 39891/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 98% (8 cores) Memory: 39894/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 72% (8 cores) Memory: 39745/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Running SVTyper on Delly outputs grep: svtype_delly_0: Is a directory CPU: 90% (8 cores) Memory: 43951/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 40669/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 36118/67740MB Storage: 1623GB free Net: 0↓/0↑MBps grep: svtype_delly_1: Is a directory CPU: 72% (8 cores) Memory: 34478/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 97% (8 cores) Memory: 36306/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 94% (8 cores) Memory: 34479/67740MB Storage: 1623GB free Net: 0↓/0↑MBps grep: svtype_delly_2: Is a directory grep: svtype_delly_3: Is a directory CPU: 72% (8 cores) Memory: 46220/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 39732/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 45024/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 46119/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 38280/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 46385/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 43861/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 39689/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 46824/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 36208/67740MB Storage: 1623GB free Net: 0↓/0↑MBps CPU: 31% (8 cores) Memory: 34097/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Running SVTyper on Lumpy outputs grep: svtype_lumpy: Is a directory CPU: 12% (8 cores) Memory: 32544/67740MB Storage: 1623GB free Net: 0↓/0↑MBps Running SVTyper on Manta outputs DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. Preparing inputs for SURVIVOR Adding parliament2Tumor.breakdancer.svtyped.vcf to SURVIVOR inputs Adding parliament2Tumor.cnvnator.svtyped.vcf to SURVIVOR inputs Adding parliament2Tumor.delly.svtyped.vcf to SURVIVOR inputs Adding parliament2Tumor.lumpy.svtyped.vcf to SURVIVOR inputs Adding parliament2Tumor.manta.svtyped.vcf to SURVIVOR inputs Running SURVIVOR merging entries: 91847 merging entries: 1496 merging entries: 6795 merging entries: 0 merging entries: 260 Running svviz Only visualizing validated candidates sudo invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=-999 Out of memory: Kill process 12467 (svviz) score 112 or sacrifice child Killed process 12467 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:388kB tail invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 12408 (svviz) score 112 or sacrifice child Killed process 12408 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB svviz invoked oom-killer: gfp_mask=0x2400840, order=0, oom_score_adj=0 Out of memory: Kill process 12485 (svviz) score 112 or sacrifice child Killed process 12485 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB ruby invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 12496 (svviz) score 112 or sacrifice child Killed process 12496 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB svviz invoked oom-killer: gfp_mask=0x2400840, order=0, oom_score_adj=0 Out of memory: Kill process 12525 (svviz) score 112 or sacrifice child Killed process 12525 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB dockerd invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 12533 (svviz) score 112 or sacrifice child Killed process 12533 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB svviz invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 12537 (svviz) score 112 or sacrifice child Killed process 12537 (svviz) total-vm:8384708kB, anon-rss:7820144kB, file-rss:0kB CPU: 62% (8 cores) Memory: 63674/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 91% (8 cores) Memory: 57809/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 94% (8 cores) Memory: 30723/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 30753/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 30893/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 30894/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 30809/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 30861/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 29372/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 94% (8 cores) Memory: 31015/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 30957/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 30890/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 30931/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 31071/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 30945/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 31077/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 92% (8 cores) Memory: 14309/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14328/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14363/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14407/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14397/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14425/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14419/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14450/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14470/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14471/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14517/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14555/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14534/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14574/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14573/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14610/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14627/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14649/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14651/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14681/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14692/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14740/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14687/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14714/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14764/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14782/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14777/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14800/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14823/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 14806/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 83% (8 cores) Memory: 15014/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 90% (8 cores) Memory: 63775/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 95% (8 cores) Memory: 61613/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 87% (8 cores) Memory: 59023/67740MB Storage: 1622GB free Net: 0↓/0↑MBps svviz invoked oom-killer: gfp_mask=0x24280ca, order=0, oom_score_adj=0 Out of memory: Kill process 12568 (svviz) score 78 or sacrifice child Killed process 12568 (svviz) total-vm:5983820kB, anon-rss:5415768kB, file-rss:340kB CPU: 89% (8 cores) Memory: 55276/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 91% (8 cores) Memory: 65681/67740MB Storage: 1622GB free Net: 0↓/0↑MBps svviz invoked oom-killer: gfp_mask=0x24280ca, order=0, oom_score_adj=0 Out of memory: Kill process 29947 (svviz) score 51 or sacrifice child Killed process 29947 (svviz) total-vm:3992952kB, anon-rss:3583808kB, file-rss:0kB svviz invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 22793 (svviz) score 52 or sacrifice child Killed process 22793 (svviz) total-vm:3956116kB, anon-rss:3617696kB, file-rss:24kB python invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=-999 Out of memory: Kill process 29946 (svviz) score 51 or sacrifice child Killed process 29946 (svviz) total-vm:3996692kB, anon-rss:3589804kB, file-rss:0kB ruby invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 23119 (svviz) score 51 or sacrifice child Killed process 23119 (svviz) total-vm:3936184kB, anon-rss:3597624kB, file-rss:8kB svviz invoked oom-killer: gfp_mask=0x24201ca, order=0, oom_score_adj=0 Out of memory: Kill process 23129 (svviz) score 53 or sacrifice child Killed process 23129 (svviz) total-vm:4046272kB, anon-rss:3707952kB, file-rss:0kB CPU: 90% (8 cores) Memory: 54049/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 92% (8 cores) Memory: 48994/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 92% (8 cores) Memory: 49327/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 90% (8 cores) Memory: 56696/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 94% (8 cores) Memory: 56093/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 94% (8 cores) Memory: 56831/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 93% (8 cores) Memory: 53685/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 93% (8 cores) Memory: 46556/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 93% (8 cores) Memory: 63102/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 91% (8 cores) Memory: 43367/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 91% (8 cores) Memory: 39843/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 93% (8 cores) Memory: 35235/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 96% (8 cores) Memory: 35291/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 84% (8 cores) Memory: 22502/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 71% (8 cores) Memory: 22624/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 39% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19296/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19296/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19296/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19296/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 cores) Memory: 19297/67740MB Storage: 1622GB free Net: 0↓/0↑MBps CPU: 0% (8 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slzarate commented 5 years ago

Should be resolved in the above PR