Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Fatal error :Exit code 1
0
gravatar for annet.kyomuhangi
11 months ago by
annet.kyomuhangi • 10
annet.kyomuhangi • 10 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 • 1.0k views
ADD COMMENT • link •
modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by annet.kyomuhangi • 10
0
gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 11 months ago • written 11 months ago by annet.kyomuhangi • 10

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 REPLY • link modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour