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Question: BAM files cannot be downloaded and failed MergeSamFiles Fatal error: Exit code 127 ()
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gravatar for mychung
9 months ago by
mychung • 0
Taiwan
mychung • 0 wrote:

Hi, I've mapped some WES and WGS data through the pipeline.

For the past two days, either the "merge" of mapped bam files cannot be performed or the merged, sorted, markduplicates, cleaned datasets cannot be downloaded. The .bam files can be visualized locally and they are fine.

Note: 1. .bai can be downloaded. 2. remarks under the cleaned datasets "Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/018/256/18256799/_job_tmp -Xmx7g -Xms256m ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.plant_tribes Traceback (most recent call last): File "/cvmfs/" 3. remarks for failed merge "Fatal error: Exit code 127 () /galaxy-repl/main/jobdir/018/280/18280471/tool_script.sh: line 9: picard: command not found"

Please help.

Thank you very much in advance.
bam • 399 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by mychung • 0

I'm also unable to download bam files, and am getting fatal errors for mapping with BWA. Someone else, too.

ADD REPLY • link written 9 months ago by gacarson • 10
0
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The public Main Galaxy server at https://usegalaxy.org is presenting with job errors across many tools at this time. We are actively working to correct the issues.

Please follow this ticket for updates: https://biostar.usegalaxy.org/p/26580/

Once the server is corrected, retest your specific issue and comment here in your original post if the problems persist and we can troubleshoot the use case.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k

My jobs appear to be running fine now. However, .bam files still cannot be downloaded.

ADD REPLY • link written 9 months ago by mychung • 0
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