ERROR: Cannot run mmseqs | but I can use mmseqs

[wuyudelan]

OrthoFinder version 2.5.4 installed by conda:

$ orthofinder -f rep_type_out_more_genomes_faa -M msa -S mmseqs -a 10 -o rep_type_out_more_genomes_faa_orthofinder_test

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-03-30 17:21:32 : Starting OrthoFinder 2.5.4
176 thread(s) for highly parallel tasks (BLAST searches etc.)
10 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------

ERROR: Cannot run mmseqs
Format of make database command:
  mmseqs createdb INPUT OUTPUT.fa ; mmseqs createindex OUTPUT.fa /tmp
ERROR: Cannot run mmseqs
Format of search database command:
  mmseqs search /mmseqsDBINPUT DATABASE.fa OUTPUT.db /tmp/tmpOUTPUT  --threads 1 ; mmseqs convertalis --threads 1 /mmseqsDBINPUT DATABASE.fa OUTPUT.db OUTPUT
Please check mmseqs is installed and that the executables are in the system path

ERROR: An error occurred, ***please review the error messages*** they may contain useful information about the problem.

However, conda has installed mmseqs, I can also run it with one of the seq files.

$ mmseqs createdb rep_type_out_more_genomes_faa/Type_Tetragenococcus_solitarius_NBRC_100494_GCA_001544195.1_protein.faa ./test.fa
createdb rep_type_out_more_genomes_faa/Type_Tetragenococcus_solitarius_NBRC_100494_GCA_001544195.1_protein.faa ./test.fa

MMseqs Version:         13.45111
Database type           0
Shuffle input database  true
Createdb mode           0
Write lookup file       1
Offset of numeric ids   0
Compressed              0
Verbosity               3

Converting sequences
[2425] 0s 63ms
Time for merging to test.fa_h: 0h 0m 0s 18ms
Time for merging to test.fa: 0h 0m 0s 10ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 125ms

$ mmseqs createindex test.fa /temp
createindex test.fa /temp

MMseqs Version:             13.45111
Seed substitution matrix    nucl:nucleotide.out,aa:VTML80.out
k-mer length                0
Alphabet size               nucl:5,aa:21
Compositional bias          1
Max sequence length         65535
Max results per query       300
Mask residues               1
Mask lower case residues    0
Spaced k-mers               1
Spaced k-mer pattern
Sensitivity                 7.5
k-score                     0
Check compatible            0
Search type                 0
Split database              0
Split memory limit          0
Verbosity                   3
Threads                     176
Min codons in orf           30
Max codons in length        32734
Max orf gaps                2147483647
Contig start mode           2
Contig end mode             2
Orf start mode              1
Forward frames              1,2,3
Reverse frames              1,2,3
Translation table           1
Translate orf               0
Use all table starts        false
Offset of numeric ids       0
Create lookup               0
Compressed                  0
Add orf stop                false
Overlap between sequences   0
Sequence split mode         1
Header split mode           0
Strand selection            1
Remove temporary files      false
Cannot create temporary directory /temp

Update mmseqs with conda can not fix it.

After update, MMseqs2 Version: 13.45111

[zkstewart]

Also encountering the same issue. mmseqs is available through my path, but OrthoFinder doesn't agree giving the error posted above.

I'm using the recent glibc release for v2.5.4.

[mat43672]

Hello, I have the same issue with 2.5.4 when using the Docker container davidemms/orthofinder:2.5.4

Any update on that problem ?

[Dabaixian]

Hello, i also met this problem. Does anyone know how to solve this problem(灬ꈍ ꈍ灬)

[davidecarlson]

I'm also experiencing this issue with Orthofinder 2.5.4 and mmseqs2 14.7e284 (the latest release).

Is Orthofinder tied to a particular mmseqs2 version?

[davidecarlson]

Looks like this is fixed in the code, but there has not been a release that includes the fix. Cloning the repository and running the orthofinder.py script from the cloned repo solves the issue.

[dadrasarmin]

Hi,

I had the same problem and I tried to update to the latest version as suggested by @davidecarlson. However, that did not solved my problem. But I changed something in the config file and now I can use mmseq. I did the following:

I replaced tmp in lines 58 and 59 of scripts_of/config.json with ./tmp

The good thing is that, I can run Orthofinder with mmseq. The bad thing is that I have to remove the tmp folder manually afterwards. I am using a server and I noticed the problem is permissions of tmp folder.