[svtoolkit-help] Error writing to histogram file
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[svtoolkit-help] Error writing to histogram file
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From: Noll, A. <an...@cm...> - 2013-12-20 19:50:57
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This is in response to issue # 31773145 (no e-mail has shown up in my inbox yet that I could respond to as part of the list yet?)
To answer your questions:
1) The analysis directory was clean at start of the run
2) I have seen this error on and off SGE but in all cases I was using make to kick it off
3) There was a .fail file in the metadata directory
To rule out a potential timing issue I created a new directory and then attempted to run each Preprocess step individually.
Progress was made until Preprocess step 3 where there was an error related to writing the histogram file.
I have seen this error before but mainly when more than one instance of svtoolkit was running out of the same directory. (i.e. it resolved when sequential processing was used)
For the most part everything was stable until recently migrating to the most recent version of svtoolkit...
Error text is at top and entire log below that.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Error writing to histogram file: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:75)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:26)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:123)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:59)
Caused by: java.io.FileNotFoundException: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile.addHistogram(InsertSizeHistogramFile.java:58)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:71)
... 10 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-g5671483):
##### ERROR
##### ERROR Please check the documentation guide to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Error writing to histogram file: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin
##### ERROR ------------------------------------------------------------------------------------------
INFO 12:45:09,420 HelpFormatter - ----------------------------------------------------------------
INFO 12:45:09,423 HelpFormatter - Program Name: org.broadinstitute.sv.apps.CreateMetaDataDirectory
DEBUG 12:45:09,423 HelpFormatter - Current directory: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit
INFO 12:45:09,429 HelpFormatter - Program Args: -l DEBUG -md /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata
INFO 12:45:09,429 HelpFormatter - Date/Time: 2013/12/20 12:45:09
INFO 12:45:09,429 HelpFormatter - ----------------------------------------------------------------
INFO 12:45:09,429 HelpFormatter - ----------------------------------------------------------------
INFO 12:45:09,465 MetaData - Opening metadata ...
INFO 12:45:09,465 MetaData - Adding metadata directory /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata ...
INFO 12:45:09,466 MetaData - Opened metadata.
INFO 12:45:09,470 CommandLineProgram - Program completed.
INFO 12:46:18,134 HelpFormatter - -----------------------------------------------------------
INFO 12:46:18,136 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGenomeSizes
INFO 12:46:18,139 HelpFormatter - Program Args: -O /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/genome_sizes.txt -R /home/anoll/sim/genomeSim/fasta/homo.sapiens.GRCh37.fa -ploidyMapFile /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/data/humgen_g1k_v37_ploidy.map -genomeMaskFile /home/anoll/sim/genomeSim/fasta/homo.sapiens.GRCh37.fa
INFO 12:46:18,140 HelpFormatter - Date/Time: 2013/12/20 12:46:18
INFO 12:46:18,140 HelpFormatter - -----------------------------------------------------------
INFO 12:46:18,140 HelpFormatter - -----------------------------------------------------------
INFO 12:46:18,147 ComputeGenomeSizes - Processing interval 10:1-135534747 ...
INFO 12:46:24,128 ComputeGenomeSizes - Processing interval 11:1-135006516 ...
INFO 12:46:29,681 ComputeGenomeSizes - Processing interval 12:1-133851895 ...
INFO 12:46:35,197 ComputeGenomeSizes - Processing interval 13:1-115169878 ...
INFO 12:46:39,973 ComputeGenomeSizes - Processing interval 14:1-107349540 ...
INFO 12:46:44,384 ComputeGenomeSizes - Processing interval 15:1-102531392 ...
INFO 12:46:48,623 ComputeGenomeSizes - Processing interval 16:1-90354753 ...
INFO 12:46:52,361 ComputeGenomeSizes - Processing interval 17:1-81195210 ...
INFO 12:46:55,680 ComputeGenomeSizes - Processing interval 18:1-78077248 ...
INFO 12:46:58,827 ComputeGenomeSizes - Processing interval 19:1-59128983 ...
INFO 12:47:01,193 ComputeGenomeSizes - Processing interval 1:1-249250621 ...
INFO 12:47:11,238 ComputeGenomeSizes - Processing interval 20:1-63025520 ...
INFO 12:47:13,750 ComputeGenomeSizes - Processing interval 21:1-48129895 ...
INFO 12:47:15,676 ComputeGenomeSizes - Processing interval 22:1-51304566 ...
INFO 12:47:17,714 ComputeGenomeSizes - Processing interval 2:1-243199373 ...
INFO 12:47:27,781 ComputeGenomeSizes - Processing interval 3:1-198022430 ...
INFO 12:47:35,980 ComputeGenomeSizes - Processing interval 4:1-191154276 ...
INFO 12:47:43,879 ComputeGenomeSizes - Processing interval 5:1-180915260 ...
INFO 12:47:51,341 ComputeGenomeSizes - Processing interval 6:1-171115067 ...
INFO 12:47:58,481 ComputeGenomeSizes - Processing interval 7:1-159138663 ...
INFO 12:48:05,076 ComputeGenomeSizes - Processing interval 8:1-146364022 ...
INFO 12:48:11,058 ComputeGenomeSizes - Processing interval 9:1-141213431 ...
INFO 12:48:16,863 ComputeGenomeSizes - Processing interval X:1-155270560 ...
INFO 12:48:23,330 ComputeGenomeSizes - Processing interval Y:1-59373566 ...
INFO 12:48:25,831 ComputeGenomeSizes - maskedSizeMale=5979749735; maskedSizeFemale=6072607692
INFO 12:48:25,831 ComputeGenomeSizes - nonGapSizeMale=5545900142; nonGapSizeFemale=5671347136
INFO 12:48:25,919 CommandLineProgram - Program completed.
INFO 12:51:04,066 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:51:04,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-g5671483, Compiled 2013/09/01 11:04:38
INFO 12:51:04,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:51:04,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:51:04,072 HelpFormatter - Program Args: -T ComputeInsertSizeHistogramsWalker -R /home/anoll/sim/genomeSim/fasta/homo.sapiens.GRCh37.fa -O /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin -disableGATKTraversal true -md /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata -createEmpty
INFO 12:51:04,072 HelpFormatter - Date/Time: 2013/12/20 12:51:04
INFO 12:51:04,072 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:51:04,072 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:51:04,203 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:51:04,293 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 12:51:04,353 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files
INFO 12:51:04,401 GenomeAnalysisEngine - Done creating shard strategy
INFO 12:51:04,401 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:51:04,401 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 12:51:04,402 MetaData - Opening metadata ...
INFO 12:51:04,403 MetaData - Adding metadata directory /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata ...
INFO 12:51:04,404 MetaData - Opened metadata.
INFO 12:51:34,406 ProgressMeter - Starting 0.00e+00 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
INFO 12:52:04,408 ProgressMeter - Starting 0.00e+00 60.0 s 99.2 w 100.0% 60.0 s 0.0 s
INFO 12:52:34,410 ProgressMeter - Starting 0.00e+00 90.0 s 148.8 w 100.0% 90.0 s 0.0 s
INFO 12:53:04,411 ProgressMeter - Starting 0.00e+00 120.0 s 198.4 w 100.0% 120.0 s 0.0 s
INFO 12:53:34,412 ProgressMeter - Starting 0.00e+00 2.5 m 248.0 w 100.0% 2.5 m 0.0 s
INFO 12:54:04,414 ProgressMeter - Starting 0.00e+00 3.0 m 297.6 w 100.0% 3.0 m 0.0 s
INFO 12:54:34,415 ProgressMeter - Starting 0.00e+00 3.5 m 347.2 w 100.0% 3.5 m 0.0 s
INFO 12:55:04,417 ProgressMeter - Starting 0.00e+00 4.0 m 396.9 w 100.0% 4.0 m 0.0 s
INFO 12:55:34,418 ProgressMeter - Starting 0.00e+00 4.5 m 446.5 w 100.0% 4.5 m 0.0 s
INFO 12:56:04,419 ProgressMeter - Starting 0.00e+00 5.0 m 496.1 w 100.0% 5.0 m 0.0 s
INFO 12:56:34,421 ProgressMeter - Starting 0.00e+00 5.5 m 545.7 w 100.0% 5.5 m 0.0 s
INFO 12:57:04,422 ProgressMeter - Starting 0.00e+00 6.0 m 595.3 w 100.0% 6.0 m 0.0 s
INFO 12:57:34,424 ProgressMeter - Starting 0.00e+00 6.5 m 644.9 w 100.0% 6.5 m 0.0 s
INFO 12:58:04,425 ProgressMeter - Starting 0.00e+00 7.0 m 694.5 w 100.0% 7.0 m 0.0 s
INFO 12:58:34,426 ProgressMeter - Starting 0.00e+00 7.5 m 744.1 w 100.0% 7.5 m 0.0 s
INFO 12:59:04,427 ProgressMeter - Starting 0.00e+00 8.0 m 793.7 w 100.0% 8.0 m 0.0 s
INFO 12:59:34,428 ProgressMeter - Starting 0.00e+00 8.5 m 843.3 w 100.0% 8.5 m 0.0 s
INFO 13:00:04,430 ProgressMeter - Starting 0.00e+00 9.0 m 892.9 w 100.0% 9.0 m 0.0 s
INFO 13:00:34,431 ProgressMeter - Starting 0.00e+00 9.5 m 942.5 w 100.0% 9.5 m 0.0 s
INFO 13:01:04,434 ProgressMeter - Starting 0.00e+00 10.0 m 992.1 w 100.0% 10.0 m 0.0 s
INFO 13:01:34,435 ProgressMeter - Starting 0.00e+00 10.5 m 1041.7 w 100.0% 10.5 m 0.0 s
INFO 13:02:04,436 ProgressMeter - Starting 0.00e+00 11.0 m 1091.3 w 100.0% 11.0 m 0.0 s
INFO 13:02:34,437 ProgressMeter - Starting 0.00e+00 11.5 m 1140.9 w 100.0% 11.5 m 0.0 s
INFO 13:03:04,438 ProgressMeter - Starting 0.00e+00 12.0 m 1190.5 w 100.0% 12.0 m 0.0 s
INFO 13:03:34,441 ProgressMeter - Starting 0.00e+00 12.5 m 1240.1 w 100.0% 12.5 m 0.0 s
INFO 13:04:04,442 ProgressMeter - Starting 0.00e+00 13.0 m 1289.8 w 100.0% 13.0 m 0.0 s
INFO 13:04:34,443 ProgressMeter - Starting 0.00e+00 13.5 m 1339.4 w 100.0% 13.5 m 0.0 s
INFO 13:05:04,445 ProgressMeter - Starting 0.00e+00 14.0 m 1389.0 w 100.0% 14.0 m 0.0 s
INFO 13:05:34,446 ProgressMeter - Starting 0.00e+00 14.5 m 1438.6 w 100.0% 14.5 m 0.0 s
INFO 13:06:04,447 ProgressMeter - Starting 0.00e+00 15.0 m 1488.2 w 100.0% 15.0 m 0.0 s
INFO 13:06:34,448 ProgressMeter - Starting 0.00e+00 15.5 m 1537.8 w 100.0% 15.5 m 0.0 s
INFO 13:07:04,449 ProgressMeter - Starting 0.00e+00 16.0 m 1587.4 w 100.0% 16.0 m 0.0 s
INFO 13:07:34,450 ProgressMeter - Starting 0.00e+00 16.5 m 1637.0 w 100.0% 16.5 m 0.0 s
INFO 13:08:04,451 ProgressMeter - Starting 0.00e+00 17.0 m 1686.6 w 100.0% 17.0 m 0.0 s
INFO 13:08:34,452 ProgressMeter - Starting 0.00e+00 17.5 m 1736.2 w 100.0% 17.5 m 0.0 s
INFO 13:09:04,453 ProgressMeter - Starting 0.00e+00 18.0 m 1785.8 w 100.0% 18.0 m 0.0 s
INFO 13:09:34,454 ProgressMeter - Starting 0.00e+00 18.5 m 1835.4 w 100.0% 18.5 m 0.0 s
INFO 13:10:04,455 ProgressMeter - Starting 0.00e+00 19.0 m 1885.0 w 100.0% 19.0 m 0.0 s
INFO 13:10:34,456 ProgressMeter - Starting 0.00e+00 19.5 m 1934.6 w 100.0% 19.5 m 0.0 s
INFO 13:11:04,457 ProgressMeter - Starting 0.00e+00 20.0 m 1984.2 w 100.0% 20.0 m 0.0 s
INFO 13:11:34,458 ProgressMeter - Starting 0.00e+00 20.5 m 2033.8 w 100.0% 20.5 m 0.0 s
INFO 13:12:04,459 ProgressMeter - Starting 0.00e+00 21.0 m 2083.4 w 100.0% 21.0 m 0.0 s
INFO 13:12:34,460 ProgressMeter - Starting 0.00e+00 21.5 m 2133.0 w 100.0% 21.5 m 0.0 s
INFO 13:13:04,461 ProgressMeter - Starting 0.00e+00 22.0 m 2182.6 w 100.0% 22.0 m 0.0 s
INFO 13:13:34,462 ProgressMeter - Starting 0.00e+00 22.5 m 2232.2 w 100.0% 22.5 m 0.0 s
INFO 13:14:04,464 ProgressMeter - Starting 0.00e+00 23.0 m 2281.8 w 100.0% 23.0 m 0.0 s
INFO 13:14:34,465 ProgressMeter - Starting 0.00e+00 23.5 m 2331.5 w 100.0% 23.5 m 0.0 s
INFO 13:15:04,466 ProgressMeter - Starting 0.00e+00 24.0 m 2381.1 w 100.0% 24.0 m 0.0 s
INFO 13:15:34,467 ProgressMeter - Starting 0.00e+00 24.5 m 2430.7 w 100.0% 24.5 m 0.0 s
INFO 13:16:04,468 ProgressMeter - Starting 0.00e+00 25.0 m 2480.3 w 100.0% 25.0 m 0.0 s
INFO 13:16:34,469 ProgressMeter - Starting 0.00e+00 25.5 m 2529.9 w 100.0% 25.5 m 0.0 s
INFO 13:17:04,470 ProgressMeter - Starting 0.00e+00 26.0 m 2579.5 w 100.0% 26.0 m 0.0 s
INFO 13:17:34,472 ProgressMeter - Starting 0.00e+00 26.5 m 2629.1 w 100.0% 26.5 m 0.0 s
INFO 13:18:04,473 ProgressMeter - Starting 0.00e+00 27.0 m 2678.7 w 100.0% 27.0 m 0.0 s
INFO 13:18:34,474 ProgressMeter - Starting 0.00e+00 27.5 m 2728.3 w 100.0% 27.5 m 0.0 s
INFO 13:19:04,475 ProgressMeter - Starting 0.00e+00 28.0 m 2777.9 w 100.0% 28.0 m 0.0 s
INFO 13:19:34,476 ProgressMeter - Starting 0.00e+00 28.5 m 2827.5 w 100.0% 28.5 m 0.0 s
INFO 13:20:04,477 ProgressMeter - Starting 0.00e+00 29.0 m 2877.1 w 100.0% 29.0 m 0.0 s
INFO 13:20:34,478 ProgressMeter - Starting 0.00e+00 29.5 m 2926.7 w 100.0% 29.5 m 0.0 s
INFO 13:21:04,479 ProgressMeter - Starting 0.00e+00 30.0 m 2976.3 w 100.0% 30.0 m 0.0 s
INFO 13:21:34,480 ProgressMeter - Starting 0.00e+00 30.5 m 3025.9 w 100.0% 30.5 m 0.0 s
INFO 13:22:04,484 ProgressMeter - Starting 0.00e+00 31.0 m 3075.5 w 100.0% 31.0 m 0.0 s
INFO 13:22:34,485 ProgressMeter - Starting 0.00e+00 31.5 m 3125.1 w 100.0% 31.5 m 0.0 s
INFO 13:23:04,486 ProgressMeter - Starting 0.00e+00 32.0 m 3174.7 w 100.0% 32.0 m 0.0 s
INFO 13:23:34,488 ProgressMeter - Starting 0.00e+00 32.5 m 3224.3 w 100.0% 32.5 m 0.0 s
INFO 13:24:04,489 ProgressMeter - Starting 0.00e+00 33.0 m 3274.0 w 100.0% 33.0 m 0.0 s
INFO 13:24:34,490 ProgressMeter - Starting 0.00e+00 33.5 m 3323.6 w 100.0% 33.5 m 0.0 s
INFO 13:24:58,780 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Error writing to histogram file: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:75)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:26)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:123)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:59)
Caused by: java.io.FileNotFoundException: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile.addHistogram(InsertSizeHistogramFile.java:58)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:71)
... 10 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-g5671483):
##### ERROR
##### ERROR Please check the documentation guide to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Error writing to histogram file: /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/simHetHomoTest2/metadata/isd/sampleC_7723_del_40.align.sorted.hist.bin
##### ERROR ------------------------------------------------------------------------------------------
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