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Metadata for ComputeGCProfiles in GenomeSTRiP

Hi there,

I'm trying to run ComputeGCProfiles from the GenomeSTRiP suite, but am running into a problem that seems to be related to the metadata. I am using the mouse mm10 genome and have built metadata files as described on the GenomeSTRiP website (http://software.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html). Nonetheless, by running the following from the command line :

java -cp /data/brickkm/genomeSTRIP/lib/SVToolkit.jar:/usr/local/apps/GATK/3.6/GenomeAnalysisTK.jar -Xmx4g org.broadinstitute.sv.apps.ComputeGCProfiles -R /data/brickkm/genomeSTRIP/accessory_files/mm10/mm10.fasta -O tst.zip --metaDataLocation /data/brickkm/genomeSTRIP/accessory_files/mm10 -l DEBUG

I get the error below .... Any suggestions ??

INFO 17:58:18,319 HelpFormatter - ----------------------------------------------------------
INFO 17:58:18,322 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles
DEBUG 17:58:18,322 HelpFormatter - Current directory: /gpfs/gsfs4/users/brickkm/genomeSTRIP/accessory_files/mm10
INFO 17:58:18,328 HelpFormatter - Program Args: -R /data/brickkm/genomeSTRIP/accessory_files/mm10/mm10.fasta -O tst.zip --metaDataLocation /data/brickkm/genomeSTRIP/accessory_files/mm10 -l DEBUG
INFO 17:58:18,335 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.16.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14.
INFO 17:58:18,335 HelpFormatter - Date/Time: 2016/10/28 17:58:18
INFO 17:58:18,335 HelpFormatter - ----------------------------------------------------------
INFO 17:58:18,337 HelpFormatter - ----------------------------------------------------------
INFO 17:58:18,339 ComputeGCProfiles - Opening reference sequence ...
INFO 17:58:18,342 ComputeGCProfiles - Opened reference sequence.
INFO 17:58:18,343 ComputeGCProfiles - Reading metadata ...
INFO 17:58:18,344 MetaData - Opening metadata ...
INFO 17:58:18,344 MetaData - Adding metadata directory /data/brickkm/genomeSTRIP/accessory_files/mm10 ...
INFO 17:58:18,347 MetaData - Opened metadata.
INFO 17:58:18,350 ComputeGCProfiles - Read metadata.
INFO 17:58:18,350 ComputeGCProfiles - Initializing algorithm ...
Exception in thread "main" java.lang.RuntimeException
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:121)
Caused by: java.lang.NullPointerException
at org.broadinstitute.sv.apps.ComputeGCProfiles.initReadCountAlgorithm(ComputeGCProfiles.java:257)
at org.broadinstitute.sv.apps.ComputeGCProfiles.initGCProfileAlgorithm(ComputeGCProfiles.java:234)
at org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:146)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more

Thanks in advance, Kevin



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