User: adrian.altenhoff

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620
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Switzerland
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4 weeks, 1 day ago
Joined:
5 years, 5 months ago
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a***************@inf.ethz.ch

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Posts by adrian.altenhoff

<prev • 80 results • page 2 of 8 • next >
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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 3 months ago by adrian.altenhoff620
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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 3 months ago by adrian.altenhoff620
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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 3 months ago by adrian.altenhoff620
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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 4 months ago by adrian.altenhoff620
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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 4 months ago by adrian.altenhoff620
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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 5 months ago by adrian.altenhoff620
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Comment: C: OMA core dumped error in a single node/machine
... Hi Andre, I had another look into your original error and tried to figure out if the value the structure points to could actually be some meaningful data, but it turns out that this is very unlikely. It's certainly not a string value and unlikely to be even a floating point value. Let me know in ca ...
written 5 months ago by adrian.altenhoff620
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Answer: A: Best way running OMA using SLURM
... Hi your command should indeed start 100 jobs of oma standalone in parallel. however the cluster configuration specifies how much resources a job should be allocated by default if not otherwise specified. I assume that your configuration allows to use a lot of resources and hence it will only start ...
written 5 months ago by adrian.altenhoff620
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Comment: C: Best way running OMA using SLURM
... There is a default parameter file that is used in case there are no arguments ...
written 5 months ago by adrian.altenhoff620
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Comment: C: OMA cannot evaluate boolean
... no worries. good to hear! ...
written 5 months ago by adrian.altenhoff620

Latest awards to adrian.altenhoff

Scholar 11 weeks ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 3 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 18 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.3 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.8 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
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 3.2 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.3 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.4 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 3.5 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 3.6 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 3.6 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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