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Commit ab40bcb3 authored by Thomas Van Parys's avatar Thomas Van Parys
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Limit numpy threads to 4 in WGD and increase starting mem (#19)

parent de4ee6c3
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main.nf
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......@@ -1094,9 +1094,9 @@ process wgd_ksd_paranome{
module 'paml'
module 'fasttree'
time '5h'
time '10h'
memory { 4.GB + 4.GB * task.attempt }
memory { 6.GB + 4.GB * task.attempt }
errorStrategy { task.attempt < 5 ? 'retry' : 'finish' }
maxRetries 4
......@@ -1111,7 +1111,7 @@ process wgd_ksd_paranome{
"""
$activate_venv
wgd ksd $mcl_file $species_cds_fasta -o . --ignore_prefixes
OMP_NUM_THREADS=4 wgd ksd $mcl_file $species_cds_fasta -o . --ignore_prefixes
mv *.ks.svg ${species}\\.ks.svg
mv *.ks.tsv ${species}\\.ks.tsv
"""
......@@ -1126,9 +1126,9 @@ process wgd_ksd_one_v_one{
module 'paml'
module 'fasttree'
time '5h'
time '10h'
memory { 4.GB + 4.GB * task.attempt }
memory { 6.GB + 4.GB * task.attempt }
errorStrategy { task.attempt < 5 ? 'retry' : 'finish' }
maxRetries 4
......@@ -1144,7 +1144,7 @@ process wgd_ksd_one_v_one{
"""
$activate_venv
wgd ksd --one_v_one $ovo_file $species_cds_fasta $db_species_cds_fasta -o .
OMP_NUM_THREADS=4 wgd ksd --one_v_one $ovo_file $species_cds_fasta $db_species_cds_fasta -o .
mv *.ks.svg ${species}_${databaseSpecies}\\.ks.svg
mv *.ks.tsv ${species}_${databaseSpecies}\\.ks.tsv
"""
......
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