User: adrian.altenhoff

Reputation:
650
Status:
Trusted
Location:
Switzerland
Scholar ID:
Google Scholar Page
Last seen:
1 week, 5 days ago
Joined:
6 years, 4 months ago
Email:
a***************@inf.ethz.ch

about me

Posts by adrian.altenhoff

<prev • 84 results • page 2 of 9 • next >
2
votes
1
answer
359
views
1
answers
Answer: A: OMA gene vs splicing variants in the output
... Hi, currently pyham does not have an option to skip some gene elements from an orthoxml file. But we agree that this is an important feature and plan to implement it in the future. As a short term fix, the easiest option in my view is to remove in the orthoxml file the elements that do not corre ...
written 13 months ago by adrian.altenhoff650
2
votes
1
answer
320
views
1
answers
Answer: A: OMA browser: finding exact genome release information
... Dear Marton, generally speaking, the weblink on the genome page should direct you to the page from where we downloaded originally the genome. Many of the older bacteria - including your Salmonella strain - come originally from Expasy's `GenomeReviews` - a service that is no longer maintained. The ...
written 13 months ago by adrian.altenhoff650
1
vote
1
answer
368
views
1
answers
Comment: C: OMA error in reading the all-against-all files
... Hi Nicki, 1) it's good that the find command did not returned any result (that means there was no pending checkpoint file). 2) which version of OMA standalone are you using? could it be the same issue than https://www.biostars.org/p/365017/ ? That should be fixed in OMA standalone 2.3.1 3) that i ...
written 13 months ago by adrian.altenhoff650
0
votes
1
answer
331
views
1
answers
Comment: C: OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Hi Sally, what you see here happens indeed much later than loading the AllAll files, so it was indeed a buffering problem. You should indeed increase the walltime limit to something bigger and your computation will hopefully nicely run through. Best wishes Adrian ...
written 13 months ago by adrian.altenhoff650
0
votes
1
answer
368
views
1
answers
Comment: C: OMA error in reading the all-against-all files
... Hi Nicki, that is indeed quite weird. Did you try starting OMA again. It should anyways generate the missing part files then, without redoing anything that has previously been computed. Could you also check if you have any checkpoint files in the AllAll directory: `find Cache/AllAll -type f -name ...
written 13 months ago by adrian.altenhoff650
2
votes
1
answer
331
views
1
answers
Answer: A: OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Hi Sally, I'm one of the developers of OMA standalone. Couldn't it be just a buffering issue of the stdout and stderr streams? Certain HPC clusters keep a large buffer before data is written to disk, and during the phase of reading these files we don't produce a lot of output... Once the process ge ...
written 13 months ago by adrian.altenhoff650
0
votes
1
answer
368
views
1
answers
Answer: A: OMA error in reading the all-against-all files
... Hi Nicki, If that file has never existed, the process should not have reached this point. There are two possibilities to check: (1) The file is usually compressed, so please check if the file `Cache/AllAll/Dimm_proteins_A/Dimm_proteins_A/part_78-177.gz` exists. This is what the process actually tri ...
written 13 months ago by adrian.altenhoff650
2
votes
1
answer
325
views
1
answers
Answer: A: Correct formatting for IDs in OMA standalone .splice files to properly identify
... Hi, yes, this is exactly what is meant with "unique prefixes of FASTA headers". You don't have to specify the full fasta headers, but the protein ID (or even parts of it) is sufficient if it identifies the protein uniquely. The All-vs-All step does not make use of the splicing information. We sti ...
written 14 months ago by adrian.altenhoff650
0
votes
2
answers
492
views
2
answers
Comment: C: OMA error - download from gene ontology not working 404
... We fixed this problem in OMA 2.3.1. Please upgrade to at least this version if you have this problem ...
written 14 months ago by adrian.altenhoff650
2
votes
1
answer
304
views
1
answers
Answer: A: Error, 'Matches sp1/sp2 have been computed\ for different version
... Hi, the error is raised if the file in Cache/DB/Echinops_telfairi.db has been changed since it has been created (right in the beginning from the the fasta file). differences are based on computing a hash value from the file, so any modification of the file (for example changing an protein ID, etc) ...
written 15 months ago by adrian.altenhoff650

Latest awards to adrian.altenhoff

Teacher 28 days ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Scholar 12 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 13 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.1 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.6 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.0 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 4.0 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.2 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.2 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 4.4 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 4.5 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 4.5 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: 1113 users visited in the last hour