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Forum: Bioinformatics 07-08-2016, 11:05 AM
Replies: 4
Views: 1,294
Posted By mcsimenc
Ok it seems I can specify which node I want to...

Ok it seems I can specify which node I want to run in using the same syntax used to specify the resource_list (the -l option) for the TORQUE qsub command in the TEdenovo.cfg resources: sections:
...
Forum: Bioinformatics 07-08-2016, 10:45 AM
Replies: 4
Views: 1,294
Posted By mcsimenc
There are 10 compute nodes, two with a queue name...

There are 10 compute nodes, two with a queue name of "performance" and two with a queue name of "default". I'm allowed to submit jobs to any queue. But MySQL is actually only installed correctly on...
Forum: Bioinformatics 07-08-2016, 10:24 AM
Replies: 4
Views: 1,294
Posted By mcsimenc
Question Help with REPET (TEdenovo, TEannot) on HPC cluster, MySQL not on all nodes

I'm trying to use REPET v2.5 in a cluster environment using TORQUE. TEdenovo.py automatically submits jobs and I want to know how to control which nodes the jobs are submitted to. TEdenovo uses MySQL...
Forum: Bioinformatics 07-07-2016, 03:33 PM
Replies: 2
Views: 1,073
Posted By mcsimenc
Hi, I had exactly the same problem. When I went...

Hi, I had exactly the same problem. When I went into the mysql database manually and deleted the tables TEdenovo.py had created (named 'jobs' and 'info_tables' I think) then ran step 2 again it got...
Forum: Bioinformatics 06-20-2016, 10:23 AM
Replies: 6
Views: 7,093
Posted By mcsimenc
Can anyone suggest an interpretation of the...

Can anyone suggest an interpretation of the following results using stringtie --merge: ?

Three stringtie assemblies with 29747, 30865, and 29863 transcripts are merged using stringtie --merge and...
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