Error in schmutzi.pl script

[maria407]

I was able to succesfully run schmutzi.pl on some samples, unfortunately i get an unusual error with some. Error: Cannot parse the contamination output file = [sample_name]_1_mtcont.out What does it mean?

[grenaud]

Dear Maria, I am teaching today and tomorrow essentially all day, just to acknowledge receipt of your issue. In the meantime, could you post the bam file somewhere and email me a link? I will delete the bam file once the issue is resolved.

Gabriel

On Tue, Jan 7, 2020 at 11:06 AM maria407 [email protected] wrote:

I was able to succesfully run schmutzi.pl on some samples, unfortunately i get an unusual error with some. Error: Cannot parse the contamination output file = BK521_1_mtcont.out What does it mean?

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[grenaud]

I have a bit more time now, could you send me the full output from the console and ideally, send me the bam file via email if possible.