[svtoolkit-help] Error running genotyping Genome Strip.

[Dani M. <dan...@bs...>]

Hello, im running Genome Strip and i had some error in genotype stage.
1st I run Preprocess and Discovery stages with some error but they are
solved when i re-run the script.
My problem starts when I run the genotype script, i dont know if the
org.broad... is bugged or what is happening. Can you help me??

This is my command line:

export SV_DIR=/gpfs/projects/bsc05/dani/Genome_Strip/svtoolkit
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVGenotyper.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R /gpfs/projects/bsc05/jordivalls/GCAT/human_ref_PANCANCER/genome.fa \
-I
/gpfs/projects/bsc05/jordivalls/new_insilico/insilico_3/fastq_bam/insilico_tumor/BAM/bam_mem/bam_merge_all/bam_recalibrator/insilico3_recalib.bam
\
-genderMapFile /gpfs/projects/bsc05/jordivalls/GCAT/GENOME_STRIP/gender.txt
\
-md
/gpfs/scratch/bsc05/bsc05832/GCAT/GCAT/GENOME_STRIP/metadata_insilico_3_nord3
\
-runDirectory
/gpfs/scratch/bsc05/bsc05832/GCAT/GCAT/GENOME_STRIP/genotyping \
-jobLogDir
/gpfs/scratch/bsc05/bsc05832/GCAT/GCAT/GENOME_STRIP/genotyping/logs \
-vcf
/gpfs/scratch/bsc05/bsc05832/GCAT/GCAT/GENOME_STRIP/svdiscovery.dels.vcf
-O
/gpfs/scratch/bsc05/bsc05832/GCAT/GCAT/GENOME_STRIP/genotyping/insilico3.genotypes.vcf
-parallelRecords 100 \
-disableGATKTraversal \
-run

And this is my error:

INFO  16:21:57,799 QCommandLine - Done with errors
##### ERROR --
##### ERROR stack trace
org.broadinstitute.gatk.queue.QException: Error adding function:
org.broadinstitute.sv.qscript.SVQScript$SVGenotyper@20e19ea
        at org.broadinstitute.gatk.queue.engine.QGraph.add(QGraph.scala:141)
        at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5$$anonfun$apply$2.apply(QCommandLine.scala:166)
        at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5$$anonfun$apply$2.apply(QCommandLine.scala:166)
        at scala.collection.immutable.List.foreach(List.scala:318)
        at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:166)
        at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:146)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at
scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
        at
org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:146)
        at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
        at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
        at
org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
        at
org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.IllegalStateException: Function should have at least
one output: CommandLineGATK
        at
org.broadinstitute.gatk.queue.function.QFunction$class.isFail(QFunction.scala:175)
        at
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK.isFail(CommandLineGATK.scala:9)
        at
org.broadinstitute.gatk.queue.engine.FunctionEdge.<init>(FunctionEdge.scala:61)
        at org.broadinstitute.gatk.queue.engine.QGraph.add(QGraph.scala:136)
        ... 14 more
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version
3.7.GS-r1748-0-g74bfe0b):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the
GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions
https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Error adding function:
org.broadinstitute.sv.qscript.SVQScript$SVGenotyper@20e19ea
##### ERROR
------------------------------------------------------------------------------------------
INFO  16:21:57,806 QCommandLine - Shutting down jobs. Please wait...
/home/bsc05/bsc05832/.lsbatch/1540218102.3326608.shell: line 34: -O:
command not found
/home/bsc05/bsc05832/.lsbatch/1540218102.3326608.shell: line 35:
-parallelRecords: command not found
"Nord3_Genomestrip_genotyping_insilico3_SVGenotyper2_.3326608.err" 57L,
5441C


Thanks for help!!!
Greetings


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