Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Unsupported Platform: SLX

dx1dx1 CambridgeMember

Hi,

I've been running Genome STRiP in parallel by chromosome. The preprocessing stage worked fine, but I get this error at Discovery (seems to happen on all chromosomes)

Do you think you could help me diagnose the problem? I'm not sure what SLX is but I have seen it in GATK-related articles.

Thanks for your time,

This is the contents of the log file:

`INFO 15:36:21,372 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:36:21,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-g5671483, Compiled 2014/07/14 10:51:38
INFO 15:36:21,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:36:21,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:36:21,379 HelpFormatter - Program Args: -T SVDiscoveryWalker -R /lustre/scratch113/projects/t19-napg/CNVs/test_yuan/data/human_g1k_v37.fasta -O /lustre/scratch113/projects/t19-napg/CNVs/test_yuan/NA_E_E_chrs/chr22/chr22discovery.unfiltered.vcf -disableGATKTraversal true -md NA_E_E_chrs/chr22/metadata -configFile conf/genstrip_parameters.txt -runDirectory NA_E_E_chrs/chr22 -genderMapFile data/gender.map -genomeMaskFile data/svmask/human_g1k_v37.mask.100.fasta -L 22 -runFilePrefix chr22discovery -searchLocus 22 -searchWindow 22 -searchMinimumSize 100 -searchMaximumSize 1000000
INFO 15:36:21,379 HelpFormatter - Date/Time: 2014/09/24 15:36:21
INFO 15:36:21,379 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:36:21,380 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:36:21,609 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:36:21,810 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 15:36:21,826 IntervalUtils - Processing 51304566 bp from intervals
INFO 15:36:21,957 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files
INFO 15:36:21,973 GenomeAnalysisEngine - Done creating shard strategy
INFO 15:36:21,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:36:21,973 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 15:36:21,977 SVDiscovery - Initializing SVDiscovery ...
INFO 15:36:21,977 SVDiscovery - Reading configuration file ...
INFO 15:36:21,981 SVDiscovery - Read configuration file.
INFO 15:36:21,981 SVDiscovery - Opening reference sequence ...
INFO 15:36:21,982 SVDiscovery - Opened reference sequence.
INFO 15:36:21,982 SVDiscovery - Opening genome mask ...
INFO 15:36:21,983 SVDiscovery - Opened genome mask.
INFO 15:36:21,983 SVDiscovery - Initializing input data set ...
INFO 15:36:33,968 SVDiscovery - Initialized data set: 253 files, 1396 read groups, 253 samples.
INFO 15:36:33,972 MetaData - Opening metadata ...
INFO 15:36:33,973 MetaData - Adding metadata directory NA_E_E_chrs/chr22/metadata ...
INFO 15:36:33,989 MetaData - Opened metadata.
INFO 15:36:34,009 SVDiscovery - Opened metadata.
INFO 15:36:34,018 MetaData - Loading insert size distributions ...
INFO 15:36:34,320 SVDiscovery - Discovery alt home filtering is disabled.
INFO 15:36:44,323 SVDiscovery - Processing locus: 22:0-0:100-1000000
INFO 15:36:44,323 SVDiscovery - Locus search window: 22:0-0
INFO 15:36:51,985 ProgressMeter - Starting 0.00e+00 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
INFO 15:37:21,998 ProgressMeter - Starting 0.00e+00 60.0 s 99.2 w 100.0% 60.0 s 0.0 s
INFO 15:37:52,014 ProgressMeter - Starting 0.00e+00 90.0 s 148.9 w 100.0% 90.0 s 0.0 s
INFO 15:38:22,024 ProgressMeter - Starting 0.00e+00 120.0 s 198.5 w 100.0% 120.0 s 0.0 s
INFO 15:38:52,039 ProgressMeter - Starting 0.00e+00 2.5 m 248.1 w 100.0% 2.5 m 0.0 s
INFO 15:39:22,054 ProgressMeter - Starting 0.00e+00 3.0 m 297.8 w 100.0% 3.0 m 0.0 s
INFO 15:39:52,064 ProgressMeter - Starting 0.00e+00 3.5 m 347.4 w 100.0% 3.5 m 0.0 s
INFO 15:40:22,084 ProgressMeter - Starting 0.00e+00 4.0 m 397.0 w 100.0% 4.0 m 0.0 s
INFO 15:40:52,099 ProgressMeter - Starting 0.00e+00 4.5 m 446.6 w 100.0% 4.5 m 0.0 s
INFO 15:41:22,104 ProgressMeter - Starting 0.00e+00 5.0 m 496.2 w 100.0% 5.0 m 0.0 s
INFO 15:41:36,760 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection timed out
INFO 15:41:36,760 HttpMethodDirector - Retrying request

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: Unsupported platform: SLX
at org.broadinstitute.sv.util.ReadPairOrientation.getOrientation(ReadPairOrientation.java:159)
at org.broadinstitute.sv.discovery.ReadPairRecordSelector.getReadPairOrientation(ReadPairRecordSelector.java:212)
at org.broadinstitute.sv.discovery.ReadPairRecordSelector.selectReadPairRecord(ReadPairRecordSelector.java:110)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processRead(DeletionDiscoveryAlgorithm.java:164)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runTraversal(DeletionDiscoveryAlgorithm.java:149)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:107)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
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.SVDiscovery.main(SVDiscovery.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-g5671483):`

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Hi, Daniel,

    The problem is that Genome STRiP doesn't recognize the value in the PL tag of your @RG headers. Presumably SLX is for Solexa. SLX isn't a valid value based on the SAM spec version dated 12 Sep 2014. I'd hate to tell you to re-header your bam files.

    Do you know where these bams came from?

    If they are from Sanger, do you know how many different aliases for "ILLUMINA" you have in use?

  • dx1dx1 CambridgeMember

    Hi Bob,
    Sorry for the delay! Yes, SLX is for Solexa, but I was using some quite old BAMs from Sanger and I'm told that newer BAMs have and will have ILLUMINA for the PL tag.

    I don't think it would be too much trouble to change the headers for the BAMs I was using, but many thanks for helping me identify the issue!

Sign In or Register to comment.