OrthoFinder
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davidemms
Orthofinder skip the alignment
OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms
2022-04-07 09:18:23 : Starting OrthoFinder 2.5.4 24 thread(s) for highly parallel tasks (BLAST searches etc.) 1 thread(s) for OrthoFinder algorithm
Checking required programs are installed
Test can run "mafft /home/dell/zhenjun/all_4/OrthoFinder/Results_Apr05_1/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok Test can run "raxml" - ok
Analysing Orthogroups
2022-04-07 09:18:26 : Starting MSA/Trees Species tree: Using 201 orthogroups with minimum of 30.9% of species having single-copy genes in any orthogroup
Inferring multiple sequence alignments for species tree
2022-04-07 09:19:05 : Done 0 of 201 2022-04-07 09:35:13 : Done 100 of 201
Inferring remaining multiple sequence alignments and gene trees
2022-04-07 09:55:56 : Done 0 of 94419
I don't know why.But Orthofinder skip the "Inferring multiple sequence alignments for species tree" stage.Then Orthonfinder will report the error such as"OGxxxx.fa"doesn't exist. Please help me!
Such as ERROR, input file does not exist: /home/dell/zhenjun/all_4/OrthoFinder/Results_Apr05_1/../Results_Apr07_8/WorkingDirectory/Alignments_ids/OG0000055.fa WARNING: Unknown caught unknown exception
Hi
Could you post the complete output please and I'll have a look.
Best wishes David
Hi
Thank you,David. I solve this problem by run Orthofider on another HPC. But I meet another problem is that i can't remove a specie form specieslist.txt.
Such as these . But this speices is still in Orthofinder next run. Please help me , Thank you!
Hi
If recommend using the example dataset to quickly test that you're doing the right thing to remove species and then do the same with your full dataset.
Best wishes David