FastOMA

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Dear maintainers, I have run FastOMA on about 2200 genomes and in order to make the run smoother I have created a customised base config. The most important change is...

ens-sb

Report step uses very large amount of memory

1

Hello, I have run FastOMA on about 2200 genomes. The inference of HOGs finished all right (with some tweaks in the resource config), however the `fastoma_report` step failed as it...

ens-sb

Irene and I modified the OrthoXML script so that it is easier to call it from the console. Please review and consider pulling

spascarelli

Recursion limit reached

17

Hello, While running FastOMA on 2200 species, I encountered another mafft segmentation fault but when I resumed nextflow it seemed to not complain about the segmentation fault but I got...

Simarpreet-Kaur-Bhurji

Avoid length limit for input fasta ids

1

The enforced length limit on the fasta IDs is annoying. https://github.com/DessimozLab/FastOMA/blob/38b299167435f16c781dfe065d96e184d6decf8d/FastOMA/check_input.py#L50 we could replace all the IDs with a lookup table. however, there are a few things to consider: -...

alpae

Hello, I am hoping to run fastOMA on a dataset of 384 proteomes on a server with 72 cpus and 756Gb RAM. When I tried to run it initially (using...

POMulhair

Hello! I am having a recursion limit issue. Here is my tree: (AMPQE,(((((BRAPUM,BRAVEN),FURPAR),(CCA3H1,CCA3H2)),ANOCA),PSETE,VARKO,CHICK,(((RATNO,MOUSE),HUMAN),(SORAR,PTEVA)))); These are all downloaded from OMA browser except for CCA3H1, CCA3H2, BRAPUM, BRAVEN, FURPAR. These are all...

srobb1

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.10.1 to 1.10.3. Release notes Sourced from pypa/gh-action-pypi-publish's releases. v1.10.3 💅 Cosmetic Output Improvements In #270, @​facutuesca💰 made a follow-up to their previous PR #250, making the...

dependabot[bot]