Small RuntimeWarning seedRatioArr
Cmd:
sonicparanoid -i ./input -o ./output -t 30 --project-id bolea_v2 --max-len-diff 0.2 --output-pairs --keep-raw-alignments |tee log
Log output:
SonicParanoid 1.2.3 will be executed with the following parameters:
Run ID: bolea_v2
Run directory: /scratch_mollison/users/30042108/paralogues/output/runs/bolea_v2
Input directory: /scratch_mollison/users/30042108/paralogues/input/
Input proteomes: 3
Output directory: /scratch_mollison/users/30042108/paralogues/output
Alignments directory: /scratch_mollison/users/30042108/paralogues/output/alignments/
Pairwise tables directory: /scratch_mollison/users/30042108/paralogues/output/runs/bolea_v2/pairwise_orthologs/
Directory with ortholog groups: /scratch_mollison/users/30042108/paralogues/output/runs/bolea_v2/ortholog_groups/
Pairwise tables database directory: /scratch_mollison/users/30042108/paralogues/output/orthologs_db/
Runs directory: /scratch_mollison/users/30042108/paralogues/output/runs/
Update run: False
Create pre-filter indexes: True
Complete overwrite: False
Re-create ortholog tables: False
CPUs: 30
Run mode: default (MMseqs2 s=4.0)
MCL inflation: 1.50
For the 3 input species 3 combinations are possible.
Total possible alignments: 9
Required alignments: 9
Required ortholog table predictions: 3
Creating 3 MMseqs2 databases...
MMseqs2 databases creation elapsed time (seconds): 13.172
Performing the required 9 MMseqs2 alignments...
All-vs-all alignments elapsed time (seconds): 2192.939
Predicting 3 ortholog tables...
Ortholog tables creation elapsed time (seconds): 9.298
Creating ortholog groups...
Creating orthology matrixes...
Ortholog matrixes creation elapsed time (seconds): 4.972
/mnt/nfs/home/30042108/.pyenv/versions/3.7.3/envs/general/lib/python3.7/site-packages/sonicparanoid/orthogroups.py:543: RuntimeWarning: invalid value encountered in true_divide
seedRatioArr = (geneCntArr - inparaCntArr)/geneCntArr
Ortholog groups creation elapsed time (seconds): 44.019
Creating file with homolog pairs...
Sorting homolog pairs...
Total orthologous relations 151663
Total elapsed time (seconds): 2261.377
Snapshot:
1 GCF_000001215.4_Release_6_plus_ISO1_MT_protein.faa 31e6b99c98ab0ddf9ba0276e4ff98964d2e6e6a9849c12c8048ca963603ce23e 20118944
2 GCF_000347755.3_Ccap_2.1_protein.faa 3c28b933375932c12e709bb24b449637c92f744b0978e94c9ab415e8d1d773c8 17430814
3 OGS1.gff3.sorted.renamed.pep dc191d97f4b530cd199ce368016a2b2bfa27b56fc31f6836b54bb27c70ce2296 16827288
output looks ok though!