Running piper

[vezzi]

This issue is linked to #3 and #2 but it adds also a new problem

This are the steps I followed to run piper:

##convert to SNPseq format —> this is not properly working refer to issue #3
sthlm2UUSNP -i ../G.Grigelioniene_14_01/  -o .
cp 140528_BC423WACXX/report.tsv .

##create xml
setupFileCreator -o pipelineSetup.xml -p G.Grigelioniene_14_01_SNPseq -s  Illumina -c NGI -a a2010002 -i /proj/a2010002/nobackup/vezzi/DATA/G.Grigelioniene_14_01_SNPseq/140528_BC423WACXX/ -r /proj/a2010002/piper_references/gatk_bundle/2.8/b37/human_g1k_v37.fasta

xml file created, only one sample and only one fastq file as specified by the tsv file. This should not compromised the ability to run Piper.

To run piper I had to change the following files in order to make it find the right folders:

/proj/a2010002/nobackup/tools/piper/globalConfig.sh
     + source /proj/a2010002/nobackup/tools/piper/globalConfig.sh
     - source globalConfig.sh
/proj/a2010002/nobackup/tools/piper/globalConfig.sh
     -  SCRIPTS_DIR="${PWD}/qscripts"
     + SCRIPTS_DIR="/proj/a2010002/nobackup/tools/piper/qscripts"

At this point all the environment variables should be OK and I should be able to run Piper but now I am getting a run time error. I got a pretty cryptic java.lang.IndexOutOfBoundsException: 0 but I have to admit that I did not explore the problem too much as Nestor is going really too slow:

~/Bin/Piper/workflows/WholeGenome.sh --xml_input pipelineSetup.xml
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/apus/h1/vezzi/Bin/Piper/Piper/Piper-v1.2.0-beta2/lib/GenomeAnalysisTK.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/apus/h1/vezzi/Bin/Piper/Piper/Piper-v1.2.0-beta2/lib/Queue.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
INFO  08:48:15,636 QScriptManager - Compiling 1 QScript
DEBUG 08:48:15,637 QScriptManager - Compilation directory: /tmp/Q-Classes-4077000734800196039
WARN  08:48:22,833 QScriptManager - there were 1 feature warning(s); re-run with -feature for details
WARN  08:48:22,837 QScriptManager - two warnings found
WARN  08:48:22,837 QScriptManager - Compile succeeded with 2 warnings
INFO  08:48:22,936 HelpFormatter - ----------------------------------------------------------------------
INFO  08:48:22,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
DEBUG 08:48:22,936 HelpFormatter - Current directory: /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01
INFO  08:48:22,937 HelpFormatter - Program Args: -S /proj/a2010002/nobackup/tools/piper/qscripts/DNABestPracticeVariantCalling.scala --xml_input pipelineSetup.xml --global_config uppmax_global_config.xml --number_of_threads 8 --scatter_gather 23 -jobRunner Drmaa -jobNative -A  -p node -N 1  --job_walltime 345600 --create_delivery -l DEBUG
INFO  08:48:22,937 HelpFormatter - Executing as vezzi@nestor1.uppmax.uu.se on Linux 2.6.32-431.20.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15.
INFO  08:48:22,938 HelpFormatter - Date/Time: 2014/07/09 08:48:22
INFO  08:48:22,938 HelpFormatter - ----------------------------------------------------------------------
INFO  08:48:22,938 HelpFormatter - ----------------------------------------------------------------------
INFO  08:48:22,947 QCommandLine - Scripting DNABestPracticeVariantCalling
INFO  08:48:42,420 QCommandLine - Done with errors
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: DNABestPracticeVariantCalling.script() threw the following exception: java.lang.IndexOutOfBoundsException: 0
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:147)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.IndexOutOfBoundsException: 0
        at scala.collection.LinearSeqOptimized$class.apply(LinearSeqOptimized.scala:52)
        at scala.collection.immutable.List.apply(List.scala:84)
        at molmed.qscripts.DNABestPracticeVariantCalling.script(DNABestPracticeVariantCalling.scala:341)
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
        ... 10 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
##### 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: Unable to execute QScript: DNABestPracticeVariantCalling.script() threw the following exception: java.lang.IndexOutOfBoundsException: 0
##### ERROR ------------------------------------------------------------------------------------------
INFO  08:48:42,427 QCommandLine - Shutting down jobs. Please wait...
DEBUG 08:48:42,434 IOUtils - Deleted /tmp/Q-Classes-4077000734800196039
mv: cannot stat `*.jobreport.*': No such file or directory

[mariogiov]

I got the same error previously -- yesterday when speaking to @vezzi he suggested this was an error thrown when there were not as many arguments passed as were expected? I don't know if this is correct but I do notice that in the command line listed here there is a -A flag passed with no actual argument:

INFO 08:48:22,937 HelpFormatter - Program Args: -S /proj/a2010002/nobackup/tools/piper/qscripts/DNABestPracticeVariantCalling.scala --xml_input pipelineSetup.xml --global_config uppmax_global_config.xml --number_of_threads 8 --scatter_gather 23 -jobRunner Drmaa -jobNative -A -p node -N 1 --job_walltime 345600 --create_delivery -l DEBUG

My own command didn't have the -A flag but maybe piper expects this?

INFO 17:55:52,460 HelpFormatter - Program Args: -S /home/mario/piper/qscripts/DNABestPracticeVariantCalling.scala --xml_input /proj/a2010002/nobackup/mario/analysis_ready/G.Grigelioniene_14_01_UUSNP/G.Grigelioniene_14_01_UUSNP_setup.xml --global_config /home/mario/piper/globalConfig.xml --number_of_threads 16 --scatter_gather 23 -jobRunner Drmaa --job_walltime 345600 -run --alignment_and_qc

This is purely speculative though.

[johandahlberg]

The key phrase here is: java.lang.IndexOutOfBoundsException: 0, so it's trying to access an array on a empty array. I have an idea of where this error might arise and I'm gonna get to it as quickly as possible.

[johandahlberg]

I'm not one hundred percent that the java.lang.IndexOutOfBoundsException: 0 is resolved. But since this could easily be related to any of the other bugs that we did resolve this week I think that it should be ok to close it. Unless @vezzi or @mariogiov protest I'm going to close this in the afternoon today.