Question: Fatal error :Exit code 1
gravatar for annet.kyomuhangi
4 weeks 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: -Xmx7g -Xms256m Exception in thread "main" htsjdk.samtools. SAMException: Cannot read non-existent file: /galaxy-repl/main/files/022/

galaxy • 96 views
ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson23k • written 4 weeks ago by annet.kyomuhangi10
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:


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:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson23k

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.


ADD REPLYlink modified 29 days ago • written 29 days 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:

ADD REPLYlink modified 28 days ago • written 28 days ago by Jennifer Hillman Jackson23k
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