User: adrian.altenhoff

Reputation:
340
Status:
Trusted
Location:
Switzerland
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 4 days ago
Joined:
3 years, 10 months ago
Email:
a***************@inf.ethz.ch

about me

Posts by adrian.altenhoff

<prev • 34 results • page 1 of 4 • next >
0
votes
2
answers
189
views
2
answers
Comment: C: grid engine problem with OMA
... you might need to give the full path to the oma-start script, i.e. `qsub ./oma-start.sh` and to make the script executable (`chmod +x oma-start.sh`) but anyways, if Alex's variant works that's perfect. ...
written 19 days ago by adrian.altenhoff340
1
vote
2
answers
189
views
2
answers
Answer: A: grid engine problem with OMA
... Hi, I think this problem is related to the way you submit the job and the specific configurations of the SGE system. I suggest you try to launch the job with a submission script, e.g. cat > ./start-oma.sh << EOF #!/bin/bash #$ -S /bin/bash # Request ten minutes of wallcl ...
written 22 days ago by adrian.altenhoff340
0
votes
2
answers
147
views
2
answers
Comment: C: Will lowering the LengthTol parameter increase false positive links in Orthology
... Dear Robert, sorry about the misunderstanding. Another parameter that you might consider lowering a bit is the "ReachabilityCutoff" or the "MinEdgeCompletenessFraction" parameter (depending whether you use top-down or bottom-up HOG inference). This might be especially helpful in case that the Brach ...
written 27 days ago by adrian.altenhoff340
1
vote
2
answers
147
views
2
answers
Answer: A: Will lowering the LengthTol parameter increase false positive links in Orthology
... Dear Robert, Disclaimer: I'm one of the developer of OMA standalone. Indeed, lowering the LengthTol parameter might generally link groups together that share only a short common domain. However, there are a few things that you could do: 1. What type of groups are you looking at. OMA Groups will b ...
written 4 weeks ago by adrian.altenhoff340
0
votes
2
answers
308
views
2
answers
Comment: C: Fail job after all vs all : Error, 'unable to ReadProgram on SLURM cluster
... yes. might be useful to check why they are failing in the scheduler's log (e.g. too little memory allocated to the process, or too little runtime reserved?). Cheers Adrian ...
written 5 weeks ago by adrian.altenhoff340
0
votes
1
answer
159
views
1
answers
Answer: A: OMA standalone, "-c" to just convert the databases AFTER all vs all
... Hi Gusa, unless you changed something on one of the genome files, this should actually not happen (do you find a file Cache/conversion.done) file? Anyways, if you didn't change any input files, then, simply start the single OMA. No need to convert the databases again or run again the parallel mode ...
written 5 weeks ago by adrian.altenhoff340
0
votes
2
answers
232
views
2
answers
Comment: C: Failure to launch OMA in array mode on SLURM cluster
... so strange! what version of slurm are you using? the cluster I have access to and where the ToyExample with your submission script works like a charm is a RedHat-Enterprise 6.7 installation with slurm 14.11.10. (you can get the slurm version with slurmctld -V) ...
written 7 weeks ago by adrian.altenhoff340
0
votes
2
answers
308
views
2
answers
Answer: A: Fail job after all vs all : Error, 'unable to ReadProgram on SLURM cluster
... Hi Gusa I'm one of the OMA maintainers. The version you are using is already a bit out-dated. The way the parallel processing of jobs has since been improved quite a bit. If possible, I suggest to upgrade OMA to the latest version. Most likely the referred chunk is corrupted, something that could ...
written 7 weeks ago by adrian.altenhoff340
2
votes
2
answers
232
views
2
answers
Answer: A: Failure to launch OMA in array mode on SLURM cluster
... Hi Jeremias, I'm one of the OMA developers. This problem is quite strange to me - it's likely to be a problem of the slurm configuration that is different than the once we've so far tested. I would like to understand the problem a bit better to improve slurm support for OMA standalone. There two th ...
written 7 weeks ago by adrian.altenhoff340
0
votes
1
answer
183
views
1
answers
Answer: A: OMA -c option Bus error
... Hi, most likely it finished fine. if the file Cache/conversion.done exists, the conversion step finished fine. Best wishes Adrian ...
written 7 weeks ago by adrian.altenhoff340

Latest awards to adrian.altenhoff

Scholar 8 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 14 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 18 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 19 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 21 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 22 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 23 months ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 2.0 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 663 users visited in the last hour