Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals.
I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: *Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): ##### ERROR The invalid argume *Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach* *
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