Brad Chapman chapmanb
chapmanb
/ hs_err-bqsr_deflater.log
Created
September 24, 2017 09:45
Java error log from BQSR core dump on GATK4 beta5
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| # | |
| # A fatal error has been detected by the Java Runtime Environment: | |
| # | |
| # SIGSEGV (0xb) at pc=0x00007f9400380c30, pid=45651, tid=0x00007f93fdbde700 | |
| # | |
| # JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01) | |
| # Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 ) | |
| # Problematic frame: | |
| # V [libjvm.so+0x617c30] InstanceKlass::oop_oop_iterate_nv(oopDesc*, FastScanClosure*)+0x1a0 | |
| # |
chapmanb
/ bcbio-commands-gatk4-joint.log
Last active
August 23, 2017 19:29
GATK4 joint and pooled calling example -- bcbio commands
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| [2017-08-23T18:20Z] zcat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-Test1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmppr3F3t/7_100326_FC6107FAAXX-Test1.vcf.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpYZCwp9/7_100326_FC6107FAAXX-Test1.vcf.gz | |
| [2017-08-23T18:20Z] bamtofastq filename=/home/chapmanb/bio/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.cram inputformat=cram T=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-s1-sort gz=1 collate=1 colsbs=1048576 exclude=SECONDARY,SUPPLEMENTARY F=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-p1.fq.gz F2=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-p2.fq.gz S=/home/chapmanb/bio/bcbio-nextgen/tests/te |
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| INFO:toil.fileStore:Starting job ('CWLGather' i/J/jobA0S4Xl) with ID (1d090beaa77a61c032c1d4bb019c6d8979951999). | |
| Traceback (most recent call last): | |
| File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/toil/worker.py", line 336, in main | |
| job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) | |
| File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/toil/job.py", line 1289, in _runner | |
| returnValues = self._run(jobGraph, fileStore) | |
| File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/toil/job.py", line 1234, in _run | |
| return self.run(fileStore) | |
| File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 520, in run | |
| for k in [shortname(i) for i in self.step.tool["out"]]: |
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| ==16320== Helgrind, a thread error detector | |
| ==16320== Copyright (C) 2007-2015, and GNU GPL'd, by OpenWorks LLP et al. | |
| ==16320== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info | |
| ==16320== Command: variant Test1-sort.bam -b -t 0 -o /dev/null | |
| ==16320== | |
| --16320-- Valgrind options: | |
| --16320-- -v | |
| --16320-- --tool=helgrind | |
| --16320-- Contents of /proc/version: | |
| --16320-- Linux version 4.4.0-59-generic (buildd@lgw01-11) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 |
chapmanb
/ iconic_ucl_pipeline_changes.diff
Created
August 15, 2017 14:51
iconic_ucl_pipeline_changes.diff
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| --- command_line_HIV_pipeline.sh.orig 2016-12-02 15:10:02.000000000 -0500 | |
| +++ command_line_HIV_pipeline.sh 2017-02-01 22:01:49.000000000 -0500 | |
| @@ -8,40 +8,65 @@ | |
| #$ -wd /path/to/working_directory | |
| #$ -t 1-400 | |
| +set -eu -o pipefail | |
| + | |
| +# Find original directory of bash script, resovling symlinks | |
| +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 |
chapmanb
/ NA12878-platinum-chr20-toil.log
Last active
May 15, 2017 18:02
Debugging job slowness in variant calling during Toil CWL runs
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| Added job: 'CWLScatter' 1/s/jobcVi2Ql to active jobs | |
| Built the jobs list, currently have 1 jobs to update and 6 jobs issued | |
| Updating status of job 'CWLScatter' 1/s/jobcVi2Ql with ID 1/s/jobcVi2Ql: with result status: 0 | |
| Job: 1/s/jobcVi2Ql has 200 successors to schedule | |
| Issuing the command: _toil_worker file:/mnt/work/bcbio_validation_workflows/NA12878-chr20/synapse/cwltoil_work/cwltoil_jobstore K/Z/jobcVvDx8 with memory: 3221225472, cores: 1, disk: 2147483648 | |
| Issued job 'file:///mnt/work/bcbio_validation_workflows/NA12878-chr20/synapse/NA12878-platinum-chr20-workflow/steps/variantcall_batch_region.cwl' bcbio_nextgen.py runfn variantcall_batch_region cwl K/Z/jobcVvDx8 with job batch system ID: 34 and cores: 1, disk: 2.0 G, and memory: 3.0 G | |
| Acquiring 3221225472 bytes of memory from a pool of 3672276992. | |
| Issuing the command: _toil_worker file:/mnt/work/bcbio_validation_workflows/NA12878-chr20/synapse/cwltoil_work/cwltoil_jobstore h/g/job1IMWzQ with memory: 3221225472, cores: 1, disk: 2147483648 | |
| Acquiring 10 frac |
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| chr1_gl000191_random 106433 3157608060 50 51 | |
| chr1_gl000192_random 547496 3157716644 50 51 | |
| chr4_ctg9_hap1 590426 3158275106 50 51 | |
| chr4_gl000193_random 189789 3158877363 50 51 | |
| chr4_gl000194_random 191469 3159070970 50 51 | |
| chr6_apd_hap1 4622290 3159266284 50 51 | |
| chr6_cox_hap2 4795371 3163981035 50 51 | |
| chr6_dbb_hap3 4610396 3168872329 50 51 | |
| chr6_mann_hap4 4683263 3173574949 50 51 | |
| chr6_mcf_hap5 4833398 3178351893 50 51 |
chapmanb
/ HCC2218-cnvkit.vcf
Created
April 19, 2017 13:32
HCC2218 validation comparisons, alternative breakends
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| ##fileformat=VCFv4.2 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##fileDate=20170404 | |
| ##source=CNVkit v0.8.5 | |
| ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> | |
| ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
| ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | |
| ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> | |
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> |
chapmanb
/ NA12878-bcbio-offtarget-regions.bed
Created
March 7, 2017 15:49
NA12878-bcbio-offtarget-regions.bed
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| 1 33476488 33476611 123 | |
| 1 33487399 33487522 123 | |
| 1 33490270 33490393 123 | |
| 1 33503580 33503703 123 | |
| 1 59096277 59096496 219 | |
| 1 167410065 167410257 192 | |
| 1 198608475 198608598 123 | |
| 1 198668910 198669033 123 | |
| 1 198671749 198671872 123 | |
| 1 198679025 198679148 123 |
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| genome | resource | version | |
|---|---|---|---|
| GRCh37 | GA4GH_problem_regions | 20160916 | |
| GRCh37 | MIG | 20150730 | |
| GRCh37 | prioritize | 20160215 | |
| GRCh37 | dbsnp | 147-20160408 | |
| GRCh37 | hapmap | 3.3 | |
| GRCh37 | 1000g_omni_snps | 2.5 | |
| GRCh37 | ACMG56_genes | 20160810 | |
| GRCh37 | 1000g_snps | 2.8 | |
| GRCh37 | mills_indels | 2.8 |