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