Galaxy MergesameFiles error on local instalation

Question: Galaxy MergesameFiles error on local instalation

3.2 years ago by

chris • 10

United Kingdom

chris • 10 wrote:

I have created a local Galaxy server and have come across a problem when using mergesamfile, this does not happen when I use the online server.

Tool execution generated the following error message:

Fatal error: Exit code 127 ()

/home/osboxes/galaxy/database/job_working_directory/000/13/galaxy_13.sh: 21: /home/osboxes/galaxy/database/job_working_directory/000/13/galaxy_13.sh: java: not found
[bam_header_read] bgzf_check_EOF: Invalid argument

The tool produced the following additional output:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.

Any suggestions, before i pull all my remaining hair out?

galaxy samtools • 1.2k views

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modified 3.2 years ago • written 3.2 years ago by chris • 10

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Start by double checking if samtools is both installed and installed correctly. This can be done in the Admin area, "Manage Installed Repositories".

Next, check that the BAM datasets all loaded correctly and completely. It should not have yellow message about metadata problems at the top of the dataset's box in the history panel.

Please let us know if these checks do not resolve the issue. We may ask for the shared history link at http://usegalaxy.org with the same analysis (the working one) to help troubleshoot, so please retain that with undeleted datasets, or you can recreate it if we need it.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

3.2 years ago by

chris • 10

United Kingdom

chris • 10 wrote:

After I posted the problem I found a solution, however I do not understand how or why it works

I believe the issue has something to do with Picards temperory files.

Here is what I did to "fix" the issue, any comments on why this has worked are welcome

1. Installed java:- default-jre

2. ran this command (which is required each time I restart):- Java -Djava.io.tmpdir=/scratch/tmp

Jennifer, thank you for taking the time to reply, the tools were installed correctly and the data was loaded correctly.

ADD COMMENT • link modified 3.2 years ago • written 3.2 years ago by chris • 10

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