Test-drive the GATK tools and Best Practices pipelines on Terra
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delete tmp files from gatk in local galaxy installation
I am trying to run Haplotype Caller from a local installation of Galaxy. After running it the first time, I changed the env.sh so it could find the .jar file for GATK. Now when I try to run it, I get the following error. I cannot locate the tmp directory to delete the file, and I don't know how to specify a different output file through Galaxy. Any help?
[Wed Jan 22 23:07:26 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-0WHp_x/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-0WHp_x/dict2435252299968971001.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Jan 22 23:07:26 CST 2014] Executing as [email protected] on Linux 3.5.0-44-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_25-b30; Picard version: null
[Wed Jan 22 23:07:26 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.