Hi ,
I have a bam file without library name , although each bam file is one library. The SVPreprocess.q throws a warning and an error in the ComputeInsertSizeHistogramsWalker and ComputeGCProfileWalker steps respectively.
Below is the warning message from ComputeInsertSizeHistogramsWalker
Error: Cannot determine library identifier for read HS2000-1273_166:4:1215:5282:36837
Header from the bam :
samtools view -H test.bam
@SQ SN:GL000216.1 LN:172294
@SQ SN:GL000215.1 LN:172545
@SQ SN:GL000205.1 LN:174588
@SQ SN:GL000219.1 LN:179198
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000223.1 LN:180455
@SQ SN:GL000195.1 LN:182896
@SQ SN:GL000212.1 LN:186858
@SQ SN:GL000222.1 LN:186861
@SQ SN:GL000200.1 LN:187035
@SQ SN:GL000193.1 LN:189789
@SQ SN:GL000194.1 LN:191469
@SQ SN:GL000225.1 LN:211173
@SQ SN:GL000192.1 LN:547496
@SQ SN:NC_007605 LN:171823
@SQ SN:hs37d5 LN:35477943
@RG ID:LP6005443-DNA_B09 SM:LP6005443-DNA_B09
@PG ID:bwa PN:bwa VN:0.7.10-r1017-dirty CL:bwa-new.kit/bwa mem -p -t4 -R@RG\tID:LP6005443-DNA_B09\tSM:LP6005443-DNA_B09 /home/hl141/bwadb/hs37d5.fa -
Is there an alternate way to specify the library information to match the read group without fixing the headers of the bam since I have to fix hundreds of bams. Also is there a hack around runinng the genotyper. Below is the stack trace I get when I run the genotyper on the same bam.
INFO 14:46:43,661 26-Oct-2015 ReadCountDiskCache - Initializing read count disk cache [/net/eichler/vol24/projects/human_diversity/nobackups/araja/GenomeSTRiP/genotyping/metadata/rccach
e.bin] ...
INFO 14:46:43,662 26-Oct-2015 ReadCountDiskCache - Read count disk cache: no cache files found.
INFO 14:46:44,786 26-Oct-2015 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.RuntimeException: Unexpected library path: LP6005443-DNA_B09/null/null
at org.broadinstitute.sv.genotyping.ReadDepthAlgorithm.initLibraryPathMap(ReadDepthAlgorithm.java:236)
at org.broadinstitute.sv.genotyping.ReadDepthAlgorithm.initialize(ReadDepthAlgorithm.java:68)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.createReadDepthAlgorithm(GenotypingDepthModule.java:1967)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.init(GenotypingDepthModule.java:1896)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initModules(GenotypingAlgorithm.java:522)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initialize(GenotypingAlgorithm.java:87)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:217)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Unexpected library path: LP6005443-DNA_B09/null/null
ERROR ------------------------------------------------------------------------------------------
Thanks in advance for the help.
Archana