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msa2profile gets "killed" when processing eggNOGDB #937

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eggrandio opened this issue Jan 20, 2025 · 0 comments
Open

msa2profile gets "killed" when processing eggNOGDB #937

eggrandio opened this issue Jan 20, 2025 · 0 comments

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@eggrandio
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Hello,

I am trying to generate databases and after downloading, for example, the eggNOGDB, I get the following error:

msa2profile /mnt/d/seq_data/tmp/14551941542608933155/msa /mnt/f/seq_data/transannot_dbs/eggNOGDB --match-mode 1 --match-ratio 0.5 --threads 32 -v 3

MMseqs Version:                 17.b804f
MSA type                        2
Substitution matrix             aa:blosum62.out,nucl:nucleotide.out
Match mode                      1
Match ratio                     0.5
Pseudo count mode               0
Pseudo count a                  substitution:1.100,context:1.400
Pseudo count b                  substitution:4.100,context:5.800
Compositional bias              1
Compositional bias              1
Global sequence weighting       false
Filter MSA                      1
Use filter only at N seqs       0
Minimum coverage                0
Minimum seq. id.                0.0
Minimum score per column        -20
Maximum seq. id. threshold      0.9
Select N most diverse seqs      1000
Gap open cost                   aa:11,nucl:5
Gap extension cost              aa:1,nucl:2
Skip query                      false
Threads                         32
Compressed                      0
Verbosity                       3

Finding maximum sequence length and set size.
Killed=================================================>          ] 84.02% 293.85K eta 3m 17s       s    

Disk space should not be an issue. Could it be memory? I see that the DB is split in several files that should fit into memory.

Any advice is welcome.

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