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picard 2.10.7 fails pipelining SortSam and SetNmAndUqTags

SkyWarriorSkyWarrior TurkeyMember ✭✭✭
edited August 2017 in Ask the GATK team

Hi. I just upgraded to picard 2.10.7 and doing my regular exome work however I noticed this problem under 2 different platforms.

18:12:17.734 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sky/scripts/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib
[Fri Aug 04 18:12:17 EET 2017] picard.sam.SortSam INPUT=Wes_marked.bam OUTPUT=/dev/stdout SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false[Fri Aug 04 18:12:17 EET 2017] picard.sam.SetNmAndUqTags INPUT=/dev/stdin OUTPUT=Wes_sorted.bam CREATE_INDEX=true REFERENCE_SEQUENCE=/Users/sky/hg19/hg19/hg19_ref-ym.fa IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false

[Fri Aug 04 18:12:17 EET 2017] Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT[Fri Aug 04 18:12:17 EET 2017] Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT

INFO 2017-08-04 18:13:32 SortSam Read 10,000,000 records. Elapsed time: 00:01:09s. Time for last 10,000,000: 69s. Last read position: chr14:89,041,316
INFO 2017-08-04 18:14:30 SortSam Read 20,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 57s. Last read position: chr19:39,516,007
INFO 2017-08-04 18:15:30 SortSam Read 30,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 59s. Last read position: chrX:12,939,808
INFO 2017-08-04 18:16:55 SortSam Read 40,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 84s. Last read position: chr6:128,840,098
INFO 2017-08-04 18:18:15 SortSam Read 50,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 80s. Last read position: chr22:38,121,640
INFO 2017-08-04 18:19:39 SortSam Read 60,000,000 records. Elapsed time: 00:07:16s. Time for last 10,000,000: 83s. Last read position: chr5:101,312,505
INFO 2017-08-04 18:21:02 SortSam Read 70,000,000 records. Elapsed time: 00:08:39s. Time for last 10,000,000: 83s. Last read position: chr21:31,661,664
INFO 2017-08-04 18:22:07 SortSam Finished reading inputs, merging and writing to output now.
[Fri Aug 04 18:22:11 EET 2017] picard.sam.SetNmAndUqTags done. Elapsed time: 9.99 minutes.
Runtime.totalMemory()=257425408
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Input must be coordinate-sorted for this program to run. Found: unsorted
at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:96)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
[Fri Aug 04 18:22:11 EET 2017] picard.sam.SortSam done. Elapsed time: 10.00 minutes.
Runtime.totalMemory()=3493855232
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /dev/stdout
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:388)
at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:351)
at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:250)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:198)
at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:142)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:135)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:226)
at picard.sam.SortSam.doWork(SortSam.java:107)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
Caused by: java.io.IOException: Broken pipe
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
... 13 more

Same problem persists under Ubuntu 17.04 with Java 1.8.0_144 as well. I am returning to 2.10.6 to see if this problem was still there.

EDIT: 2.10.6 works fine..

Best Answers

  • SkyWarriorSkyWarrior Turkey ✭✭✭
    Accepted Answer

    My findings:

    • Picard 2.10.6 works fine with pipelined SortSam and SetNmMdAndUqTags/SetNmAndUqTags at the moment.
    • Picard 2.10.7 fails both pipelined configurations.
    • Picard 2.10.7 works both configurations without pipelining.
  • SkyWarriorSkyWarrior Turkey ✭✭✭
    Accepted Answer

    Looks like the problem is solved in later versions now. I tested only 2.10.9 and pipelining works properly.

    Thanks for the help.

  • SkyWarriorSkyWarrior Turkey ✭✭✭
    edited January 2018 Accepted Answer

    Ok now things are getting more interesting. Disabling intelflaters seems to solve the problem. But why?

    Same flaters work with standalone picard as well and they don't have any issues. Compression level does not change anything. Is this a memory allocation error? I don't think so because it does not segfault. The error message says filename not found.

    I am wondering if this has anything to do with meltdown patches. Both of my systems (Ubuntu and macOS) are patched against meltdown bug. And Intel flaters are causing this issue. But this won't explain why standalone picard is still working fine with them. The only explanation that I have is the difference between HTSJDK and GKL versions between standalone picard 2.17.2 and embedded picard 2.17.2 in gatk. The latest HTSJDK update for standalone picard mentions 2.13.1 version but the one in gatk 4.0 is 2.13.2 I believe. I don't have the info about GKL version used in them.

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @SkyWarrior,

    Actually, SetNmAndUqTags has been deprecated. Please use SetNmMdAndUqTags instead. You should be able to pipe from SortSam to SetNmAndUqTags.

    In addition to testing v2.10.6 as you mention, can you see if you get the same error if you do not pipe the processes? Thanks.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Hmm good question. Also I have not noticed that the former was deprecated. I will try the new method first and then try others to debug the issue.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    2.10.7 using the new method pipelined to SortSam
    18:53:59.161 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sky/scripts/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib
    [Fri Aug 04 18:53:59 EET 2017] picard.sam.SetNmMdAndUqTags INPUT=/dev/stdin OUTPUT=Wes_sorted.bam CREATE_INDEX=true REFERENCE_SEQUENCE=/Users/sky/hg19/hg19/hg19_ref-ym.fa IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
    [Fri Aug 04 18:53:59 EET 2017] picard.sam.SortSam INPUT=Wes_marked.bam OUTPUT=/dev/stdout SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
    [Fri Aug 04 18:53:59 EET 2017] Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT
    [Fri Aug 04 18:53:59 EET 2017] Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT
    INFO 2017-08-04 18:55:07 SortSam Read 10,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 63s. Last read position: chr14:89,041,316
    INFO 2017-08-04 18:55:58 SortSam Read 20,000,000 records. Elapsed time: 00:01:53s. Time for last 10,000,000: 50s. Last read position: chr19:39,516,007
    INFO 2017-08-04 18:56:53 SortSam Read 30,000,000 records. Elapsed time: 00:02:49s. Time for last 10,000,000: 55s. Last read position: chrX:12,939,808
    INFO 2017-08-04 18:58:08 SortSam Read 40,000,000 records. Elapsed time: 00:04:04s. Time for last 10,000,000: 75s. Last read position: chr6:128,840,098
    INFO 2017-08-04 18:59:22 SortSam Read 50,000,000 records. Elapsed time: 00:05:17s. Time for last 10,000,000: 73s. Last read position: chr22:38,121,640
    INFO 2017-08-04 19:00:38 SortSam Read 60,000,000 records. Elapsed time: 00:06:34s. Time for last 10,000,000: 76s. Last read position: chr5:101,312,505
    INFO 2017-08-04 19:01:53 SortSam Read 70,000,000 records. Elapsed time: 00:07:49s. Time for last 10,000,000: 75s. Last read position: chr21:31,661,664
    INFO 2017-08-04 19:02:55 SortSam Finished reading inputs, merging and writing to output now.
    [Fri Aug 04 19:02:58 EET 2017] picard.sam.SetNmMdAndUqTags done. Elapsed time: 9.08 minutes.
    Runtime.totalMemory()=257425408
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" htsjdk.samtools.SAMException: Input must be coordinate-sorted for this program to run. Found: unsorted
    at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:96)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
    [Fri Aug 04 19:02:58 EET 2017] picard.sam.SortSam done. Elapsed time: 9.08 minutes.
    Runtime.totalMemory()=3509583872
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /dev/stdout
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
    at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:388)
    at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:351)
    at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:250)
    at java.io.DataOutputStream.write(DataOutputStream.java:107)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:198)
    at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:142)
    at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:135)
    at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:226)
    at picard.sam.SortSam.doWork(SortSam.java:107)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
    Caused by: java.io.IOException: Broken pipe
    at java.io.FileOutputStream.writeBytes(Native Method)
    at java.io.FileOutputStream.write(FileOutputStream.java:326)
    at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
    at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
    ... 13 more
    Now onto unpiped workflow.
    More tests coming along the way...

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    Accepted Answer

    My findings:

    • Picard 2.10.6 works fine with pipelined SortSam and SetNmMdAndUqTags/SetNmAndUqTags at the moment.
    • Picard 2.10.7 fails both pipelined configurations.
    • Picard 2.10.7 works both configurations without pipelining.

    Issue · Github
    by shlee

    Issue Number
    895
    State
    closed
    Last Updated
    Assignee
    Array
    Closed By
    sooheelee
  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    Accepted Answer

    Looks like the problem is solved in later versions now. I tested only 2.10.9 and pipelining works properly.

    Thanks for the help.

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Thanks for reporting back @SkyWarrior.

  • fhzhfhzh Member

    Hi guys,
    I encounter a problem with Picard SetNmMdAndUqTags.

    Here is the screenshot I got:
    [Tue Aug 22 13:35:19 EDT 2017] picard.sam.SetNmMdAndUqTags INPUT=/gpfs_common/old_share3/hfang4/GBS_data/samtools.out/sorted.NC_13_101.bam OUTPUT=/gpfs_common/old_share3/hfang4/GBS_data/samtools.out/sorted.NC_13_101.fixed.bam REFERENCE_SEQUENCE=/gpfs_common/old_share3/hfang4/GBS_data/Ghirsutum_458_v1.0.fa IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
    [Tue Aug 22 13:35:19 EDT 2017] Executing as [email protected] on Linux 3.10.0-229.1.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_31-b13; Picard version: 2.10.0-SNAPSHOT
    [Tue Aug 22 13:35:23 EDT 2017] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.06 minutes.
    Runtime.totalMemory()=1009254400
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /gpfs_common/old_share3/hfang4/GBS_data/samtools.out/sorted.NC_13_101.fixed.bam
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
    at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:388)
    at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:351)
    at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:250)
    at java.io.DataOutputStream.write(DataOutputStream.java:107)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:198)
    at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:168)
    at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:135)
    at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:201)
    at picard.sam.SetNmMdAndUqTags$$Lambda$7/433287555.accept(Unknown Source)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    at java.util.stream.ReferencePipeline$11$1.accept(ReferencePipeline.java:373)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:107)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
    Caused by: java.io.IOException: Disk quota exceeded
    at java.io.FileOutputStream.writeBytes(Native Method)
    at java.io.FileOutputStream.write(FileOutputStream.java:315)
    at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
    at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
    at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
    ... 24 more

    Does anyone have any idea how can I fix this problem?
    I am using Picard-2.10.0 and Jave 1.18 on a server.

    Thanks

    fhzh

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    I bet OpenJDK might be causing the issue but I would test this with a later version then try Oracle JDK.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @fhzh
    Hi,

    Have a look at this thread too.

    -Sheila

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Hi.

    This bug is back in GATK 4.0. Pipelining fails with the below error
    htsjdk.samtools.SAMException: Input must be coordinate-sorted for this program to run. Found: unsorted
    AFAIK picard 2.17.0 was flawless.

    Issue · Github
    by shlee

    Issue Number
    2826
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    sooheelee
  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @SkyWarrior,

    Thanks for reporting this issue. We want to get to the bottom of this. I'll need your help narrowing down where the problem might be. Here are some things to control for:

    The following statement means you tested standalone Picard v2.17.0 and it works fine, yes?

    AFAIK picard 2.17.0 was flawless.

    GATK4.0 uses Picard v2.17.2. So can you please test what happens with standalone Picard v2.17.2? Then we can narrow down the issue to Picard or GATK. Thanks.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited January 2018

    Yes I tested 2.17.0 on the same data after I wrote that line. I also used 2.17.0 on some other data as well so I am pretty confident in that. I have not tested Picard 2.17.2 as a standalone package. I will do that shortly.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited January 2018

    I completed testing with Picard 2.17.2 and GATK4.0.

    Picard 2.17.2 is fine with pipelining however GATK4.0 fails to pipeline for the same sample.

    Here is my command for GATK4.0
    set -o pipefail gatk SortSam -I $foldername'_marked.bam' -O /dev/stdout -SO coordinate | gatk SetNmMdAndUqTags -I /dev/stdin -O $foldername'_sorted.bam' --CREATE_INDEX true -R $HG19FULL

    Here is my command for Picard 2.17.2

    set -o pipefail java -jar $PICARD SortSam INPUT=$foldername'_marked.bam' OUTPUT=/dev/stdout SORT_ORDER=coordinate | java -jar $PICARD SetNmMdAndUqTags INPUT=/dev/stdin OUTPUT=$foldername'_sorted.bam' CREATE_INDEX=true R=$HG19FULL

    Picard 2.17.3 is also fine with pipelining using the same command. Looks like this is a GATK4.0 problem.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited January 2018 Accepted Answer

    Ok now things are getting more interesting. Disabling intelflaters seems to solve the problem. But why?

    Same flaters work with standalone picard as well and they don't have any issues. Compression level does not change anything. Is this a memory allocation error? I don't think so because it does not segfault. The error message says filename not found.

    I am wondering if this has anything to do with meltdown patches. Both of my systems (Ubuntu and macOS) are patched against meltdown bug. And Intel flaters are causing this issue. But this won't explain why standalone picard is still working fine with them. The only explanation that I have is the difference between HTSJDK and GKL versions between standalone picard 2.17.2 and embedded picard 2.17.2 in gatk. The latest HTSJDK update for standalone picard mentions 2.13.1 version but the one in gatk 4.0 is 2.13.2 I believe. I don't have the info about GKL version used in them.

    Issue · Github
    by shlee

    Issue Number
    4133
    State
    closed
    Last Updated
    Assignee
    Array
    Closed By
    jamesemery
  • LouisBLouisB Broad InstituteMember, Broadie, Dev ✭✭

    I opened an issue to address here: https://github.com/broadinstitute/gatk/issues/4135. Until then, could you use a named pipe instead of stdout?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Ok. That feels better.

    @shlee
    Yes. That is to remind me how my trusty workstations turned into a potato in one day - by the hand of ghosts with sticks. Yes I am observing 5 to 10 % slowdowns here and there where I have IO heavy parallel tasks running for analysis.

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