Question: Galaxy MergesameFiles error on local instalation
1
gravatar for chris
3.2 years ago by
chris10
United Kingdom
chris10 wrote:

Hi

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
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by chris10
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k
0
gravatar for chris
3.2 years ago by
chris10
United Kingdom
chris10 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 COMMENTlink modified 3.2 years ago • written 3.2 years ago by chris10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour