Question: Fatal error :Exit code 1
0
gravatar for annet.kyomuhangi
6 months ago by
annet.kyomuhangi10 wrote:

Am getting the error below with "NSG: Picard:" and am using the tool "fixmate information". What does the error mean and how can i fix it?

Thank you!

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/017/883/17883491/_job_tmp -Xmx7g -Xms256m Exception in thread "main" htsjdk.samtools. SAMException: Cannot read non-existent file: /galaxy-repl/main/files/022/

galaxy • 494 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by annet.kyomuhangi10
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This type of error with Picard tools usually means that you need to sort the BAM/SAM inputs before using the tool. This one expects a sort by queryname. There is an option on the tool form to sort, and that works fine for smaller inputs, but for larger datasets, perform the sort step prior to using this tool.

Other items to check: The inputs have more than just header content and the alignments were paired-end.

FAQs with details and other common troubleshooting solutions: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k

I tried to sort my inputs but the error is still there. I am doing variant detection, which other tools can I use besides Picard? I used BWA for mapping and it worked without any errors.

Thanks!

ADD REPLYlink modified 6 months ago • written 6 months ago by annet.kyomuhangi10

Check the BAM data. It looks like much was lost during the filtering step and these may only contain header content now. Convert with BAM-to-SAM to review.

Variant analysis tutorials are here for reference: https://galaxyproject.org/learn/

ADD REPLYlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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