problems with the varscan somatic tool

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

problems with the varscan somatic tool

karin
Dear Galaxy team,

i tried to run the varscan somatic tool from fcaramia on two pileup files but i got the following error:
Unknown Input: COMMAND::java -jar /home/karin/galaxy/dependency_dir/VarScan/2.3.5/fcaramia/varscan/51969e284317/jars/VarScan.v2.3.5.jar somatic

The command was the following:
Job Command-Line:    perl /home/karin/shed_tools/toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/51969e284317/varscan/varscan_somatic.pl "COMMAND::java -jar $JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" "NORMAL::/home/karin/galaxy-dist/database/files/000/dataset_107.dat" "TUMOR::/home/karin/galaxy-dist/database/files/000/dataset_109.dat" "OUTPUT::/home/karin/galaxy-dist/database/files/000/dataset_145.dat" "OPTION::--min-coverage 8" "OPTION::--min-coverage-normal 8" "OPTION::--min-coverage-tumor 8" "OPTION::--min-var-freq 0.1" "OPTION::--min-freq-for-hom 0.75" "OPTION::--normal-purity 1.0" "OPTION::--tumor-purity 1.0" "OPTION::--p-value 0.99" "OPTION::--somatic-p-value 0.05" "OPTION::--strand-filter 1" "OPTION::--validation 0" "OPTION::--output-vcf 1"

I also tried to change the varscan_somatic.xml file in such a way that i removed the "COMMAND::" tags etc. and used it without the varscan_somatic.pl file. After doing that, the tool ran without errors but i obtained empty files. Redoing the same command on my local computer ran properly and i obtained the wanted outputs:

java -jar $JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic /home/karin/galaxy-dist/database/files/000/dataset_107.dat /home/karin/galaxy-dist/database/files/000/dataset_109.dat dataset_131.dat --output-snp dataset_131.dat --output-indel dataset_132.dat   --min-coverage 8 --min-coverage-normal 8 --min-coverage-tumor 8 --min-var-freq 0.1 --min-freq-for-hom 0.75 --normal-purity 1.0 --tumor-purity 1.0 --p-value 0.99 --somatic-p-value 0.05 --strand-filter 1 2> testlog

in dataset_131.dat the snps, indels: dataset_132.dat, and some information (varscan directs this info on stderr) in testlog.

Any idea how to fix that? i appreciate any information on how this may be fixed!

Thanks a lot and best wishes,
Karin

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/