I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. But none of them work.
I got this error when I tried inputting one file at a time:
open: No such file or directory [bam_index_build2] fail to open the BAM file. Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/689/15689525/_galaxy_tmp -Xmx7680m -Xms256m
When I tried inputting multiple files, galaxy asked to "Verify this parameter". i.e. Input SAM/ BAM files.