User: javier.herrero

Reputation:
10
Status:
New User
Location:
Last seen:
2 years, 9 months ago
Joined:
2 years, 11 months ago
Email:
j*************@ucl.acuk

Posts by javier.herrero

<prev • 6 results • page 1 of 1 • next >
0
votes
0
answers
1.1k
views
0
answers
Comment: C: Building OMA database on SGE
... If you think that is best, I am personally fine with that. That said, I am not sure I am the most suited person to provide a tutorial on running OMA. Maybe the OMA team might want to chip in. ...
written 2.8 years ago by javier.herrero10
0
votes
0
answers
1.1k
views
0
answers
Comment: C: Buglet when running OMA on SGE
... Indeed, I am reporting this as an observation. I realise that this post is classified as a question, but I couldn't find any suitable category in the available options. I do think this is a small bug as one might want to run OMA on an SGE cluster as: 'qsub OMA -c' 'qsub -t 1-10000 OMA -s' 'qsub ...
written 2.8 years ago by javier.herrero10
2
votes
0
answers
1.1k
views
0
answers
Tutorial: Building OMA database on SGE
... There is a buglet when running OMA on SGE. This is triggered when running it as a single job. For instance, one would want to do that for building the databases with "OMA -c" or for the last step after all the "OMA -s". The error message is: > only_run_dbconv := false > Starting database co ...
oma tutorial written 2.8 years ago by javier.herrero10 • updated 2.8 years ago by genomax65k
0
votes
1
answer
948
views
1
answers
Comment: C: Error when running oma-standalone v1.0.6: Error, (in RangeOfChunk_iterator) sequ
... Hi Adrian Thank you for confirming. 200k should do the trick in my case. I was thinking that in addition to increase the limit, you could filter out long sequences at the DB building stage just as you filter short ones. This way that error would not be triggered. Regards, Javier ...
written 2.9 years ago by javier.herrero10
0
votes
1
answer
948
views
1
answers
Comment: C: Error when running oma-standalone v1.0.6: Error, (in RangeOfChunk_iterator) sequ
... Further to my previous question, I have been playing with a toy dataset. Indeed, increasing one of the sequences artificially beyond 100,000 bp seems to trigger this error. Is there any workaround or any other recommended solution apart from either truncating or completely skipping this sequence? ...
written 2.9 years ago by javier.herrero10
1
vote
1
answer
948
views
1
answer
Error when running oma-standalone v1.0.6: Error, (in RangeOfChunk_iterator) sequence 2 is too long
... Dear all I am trying to run OMA standalone on a set of primate genomes, using DNA sequences instead of AA. I am running OMA v1.0.6. Some/many of my jobs are failing with the following error message (I am using -d 3 to get more information): only_run_allall := true only_run_dbconv := false ...
orthologs oma written 2.9 years ago by javier.herrero10 • updated 2.9 years ago by adrian.altenhoff520

Latest awards to javier.herrero

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1202 users visited in the last hour