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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Error: input files #695

Open xiaoyezao opened 2 years ago

xiaoyezao commented 2 years ago

I encountered the following errors:

Inferring remaining multiple sequence alignments and gene trees
---------------------------------------------------------------
2022-05-04 07:22:10 : Done 0 of 61993
2022-05-04 15:05:39 : Done 1000 of 61993
2022-05-04 16:02:08 : Done 2000 of 61993
2022-05-04 16:34:17 : Done 3000 of 61993
2022-05-04 17:00:58 : Done 4000 of 61993
2022-05-04 17:24:06 : Done 5000 of 61993
2022-05-04 17:44:14 : Done 6000 of 61993
2022-05-04 18:04:49 : Done 7000 of 61993
2022-05-04 18:24:56 : Done 8000 of 61993
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000167.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000170.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000171.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000172.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000173.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /lustre/BIF/nobackup/feng041/project/1_asteraceae_synteny/1_orthofinder/campanulids26.pep/OrthoFinder/Results_May04/WorkingDirectory/Alignments_ids/OG0000174.fa
WARNING: Unknown caught unknown exception
2022-05-04 18:41:56 : Done 9000 of 61993
2022-05-04 18:57:35 : Done 10000 of 61993
2022-05-04 19:12:44 : Done 11000 of 61993
2022-05-04 19:27:21 : Done 12000 of 61993

In Orthogroup_Sequences/ and WorkingDirectory/Sequences_ids/, these orthogroups are there, however, in WorkingDirectory/Alignments_ids/ the OG0000167.fa has a size being 0 and the other five orthogroups do not exist.

Any idea on this?

hellopeccat commented 6 days ago

same when I using -A muscle

It appears to be weird cause I did not encounter this issue without -A muscle