Comments (2)
Jonathan-Holmes-Bioinformatics
commented on August 16, 2024
Hi cristoyerenahs,
OrthoFinder was built for handling eukaryotic genomes in smaller batches than you are working on (1000). It looks like the issue is due to the program opening to many files during its multiprocessing stage for writing the Orthogroup matrices.
I would recommend trying some of the solutions on this thread:
https://stackoverflow.com/questions/16526783/python-subprocess-too-many-open-files
Hope this helps.
from orthofinder.
davidemms
commented on August 16, 2024
Hi
You can also try the code in the branch 'linear_species_addition', which will be merged into the main branch soon. It has a solution to the problem of too many open files. You will need to install some extras python dependencies: biopython six scikit-learn.
All the best
David
from orthofinder.
Related Issues (20)
- "Invalid escape sequence" errors while starting OrthoFinder HOT 1
- Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below. HOT 1
- total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades HOT 1
- Species tree make_ultrameric.py not working HOT 1
- [Possible Bug] The `-og` option doesn't stop after inferring orthogroups HOT 1
- [Feature Request] Allow for passing options to Diamond and other dependencies HOT 1
- Single copy orthologs (SCO) are not being generated HOT 1
- not an issue, clarification wanted for which sequences are represented in orthogroups HOT 4
- what is the Orthogroup column in N*.tsv? HOT 1
- issue with running Orthofinder HOT 2
- HIV teste 1 HOT 4
- About -a option: using pre-computed BLAST results does not increase the number of orthofinder threads HOT 1
- Option to start Orthofinder at stage of inferring trees from MSAs? HOT 1
- header changed in MSA
- Diamond stuck on "Running diamond all-versus-all" HOT 1
- Option to stop Orthofinder after building the species tree? HOT 2
- Running OrthoFinder with Large Species Set (>2k) and Skipping GeneTree Construction HOT 2
- disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv HOT 5
- Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days HOT 3
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