GenomeSTRiP SVGenotyping script and alt allele alignment

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Thandeka

• March 18, 2020 13:14

Hi I'm trying to run GenomeSTRiP using cram files, I opted on using the installtest scripts that come with the GenomeSTRiP package. I have modified it to suit my dataset. The discovery.sh script runs successfully, I'm having difficulties with running the genotype.sh script, the Preprocessing step runs successfully but the Alt allele alignment step gives me the following error: [bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort! Aborted (core dumped).

Could you please help me trace what could cause such an error.

And when i try to run the CNVDiscovery script I get this error: 

INFO 14:52:13,949 HelpFormatter - Date/Time: 2020/03/18 14:52:13 INFO 14:52:13,949 HelpFormatter - ---------------------------------------------------------------------- INFO 14:52:13,949 HelpFormatter - ---------------------------------------------------------------------- INFO 14:52:13,956 QCommandLine - Scripting CNVDiscoveryStage1 INFO 14:52:14,054 QCommandLine - Added 2 functions INFO 14:52:14,062 QGraph - Generating graph. INFO 14:52:14,086 QGraph - Running jobs. ERROR 14:52:14,154 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libslurmdb.so.33: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at com.sun.jna.Native.register(Native.java:1018) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.<clinit>(LibDrmaa.java:35) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:468) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:465) at scala.collection.immutable.List.foreach(List.scala:318) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:465) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

Please help  to figureout what I am doing wrong.

 

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• 

  Bhanu Gandham

  • March 18, 2020 22:38

  Hi Thandeka

   

  I am adding Bob Handsaker to this thread. Bob will be able to help you out with this.

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  Bob Handsaker

  • March 19, 2020 04:58

  I recommend no longer running alt allele alignment. Just skip this step and the -altAlignments argument.

  By the way, the best practices are to follow the WDLs, not the installtest script.

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  Thandeka

  • March 19, 2020 06:37

  Hi Bob, thank you for the response, I'm sorry but what is  WDLs? will WDLs also help me with the CNVDiscovery?

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  Bob Handsaker

  • March 20, 2020 02:56

  WDL is a workflow description language used by terra and similar tools/environments https://app.terra.bio/

  The WDLs we use to run Genome STRiP are in the wdl directory (wdl/firecloud).

   

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