Hello Galaxy Team,

I get this error

"Error reading bam file. This usually indicates a problem with the index (bai) file. ArrayIndexOutofBoundsException: 6921 (6921)."

when I finish my pipeline and try do view any of the sam or bam files.

-occurs on both hg19 and hg_g1k_v37

-i tried to sort and index the sam file from step 22 and 25 in igv, but without success and ideally I do not want to have any steps outside Galaxy.

-I get the error on the data of step 44, 38 and 35

Opening the sam file from step 25 gives: "could not find index" and after I use the tools in IGV it works and I can look at the aligned sequences, but still this is a step outside of Galaxy, which I do not want.

Anything I overlooked? I'd appreciate every hint.

Best
Moritz