Picard error (AddOrReplaceReadGroups)

Answered

Follow

Hyesun Cho

• September 19, 2022 19:57

Picard ver : 2.27.4

command line :

java -Xmx8g -jar picard.jar AddOrReplaceReadGroups -INPUT ./Sample_L1_1_380_197_2pass/Aligned.out.sam -OUTPUT ./Sample_L1_1_380_197_2pass/Aligned.out.sorted.bam -RGID Sample_L1_1_380_197 -RGLB Sample_L1_1_380_197 -RGPL illumina -RGPU SureSelectAllExon -RGSM Sample_L1_1_380_197 

Entire log:

[Mon Sep 19 14:59:22 EDT 2022] AddOrReplaceReadGroups --INPUT ./Sample_L1_1_380_197_2pass/Aligned.out.sam --OUTPUT ./Sample_L1_1_380_197_2pass/Aligned.out.sorted.bam --RGID Sample_L1_1_380_197 --RGLB Sample_L1_1_380_197 --RGPL illumina --RGPU SureSelectAllExon --RGSM Sample_L1_1_380_197 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Sep 19 14:59:22 EDT 2022] Executing as hc828@ruddle2.ruddle.hpc.yale.internal on Linux 3.10.0-1160.62.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_322-b06; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.27.4-SNAPSHOT
INFO    2022-09-19 14:59:22    AddOrReplaceReadGroups    Created read-group ID=Sample_L1_1_380_197 PL=illumina LB=Sample_L1_1_380_197 SM=Sample_L1_1_380_197

[Mon Sep 19 14:59:23 EDT 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=16252928
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File ./Sample_L1_1_380_197_2pass/Aligned.out.sam; Line 198
Line:  --runThreadN 6 --outFileNamePrefix ./Sample_L1_1_380_197_2pass/
    at htsjdk.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:446)
    at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:231)
    at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:268)
    at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:255)
    at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:228)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:591)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:570)
    at picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:183)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

 

I don't know how to solve this problem :(

 

0

• 

  Genevieve Brandt (she/her)

  • September 20, 2022 23:57

  Hi Hyesun Cho,

  There is a tool that can help you to diagnose any issues with your sam file, called ValidateSamFile. Please take a look at this article for more details: https://gatk.broadinstitute.org/hc/en-us/articles/360035891231-Errors-in-SAM-or-BAM-files-can-be-diagnosed-with-ValidateSamFile

  Let us know if you have any questions about that!

  Best regards,

  Genevieve

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • September 27, 2022 20:37

  Hi Hyesun,

  We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

  Kind regards,

  Genevieve​

  0

  Comment actions Permalink
• 

  Hyesun Cho

  • September 27, 2022 22:07

  Thank you for your reply.

  I tried ValidateSamfile and the result was errorcode 1, and I coun't find a solution to this problem.

  I soled the problem by creating bam file directly from STAR.

   

  Best Regards,

  Hyesun

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • September 28, 2022 17:09

  Thank you for posting your solution Hyesun!

  0

  Comment actions Permalink

Please sign in to leave a comment.