wfmash killed

[mictadlo]

I tried to run wfmash with https://github.com/nf-core/pangenome --wfmash_chunks 1200. Unfortunately, the wfmash job got killed due to insufficient memory specify in the pipeline according to our sysadmin. This Nextflow pipeline version’s major advantage is that it can distribute the usually computationally heavy all versus all alignment step across a whole cluster.

I did the following steps to prepare the genomes for wfmash:

> abyss-fac ChinaLab/NbeHZ1_genome_1.0.fa JapanLab/Nbe_v1_scf.fa  LAB360/NbLab360.genome.fasta UsaLab/Niben261_genome.fasta

n     n:500 L50   min   N75   N50   N25   E-size      max   sum   name
2831  2831  10    1000  136e6 143.2e6     148.2e6     142.1e6     183.5e6     2.929e9     ChinaLab/NbeHZ1_genome_1.0.fa
1668  1668  10    1000  132.1e6     141.7e6     145e6 132.2e6     184.4e6     2.926e9     JapanLab/Nbe_v1_scf.fa
20    20    10    58.94e6     132.9e6     140.6e6     145.2e6     144.4e6     180.8e6     2.806e9     LAB360/NbLab360.genome.fasta
17639 17627 10    522   130.9e6     137.1e6     142.2e6     138.5e6     176.9e6     2.751e9     UsaLab/Niben261_genome.fasta

cat ../genomes/ChinaLab/NbeHZ1_genome_1.0.fa ../genomes/JapanLab/Nbe_v1_scf.fa ../genomes/LAB360/NbLab360.genome.fasta ../genomes/UsaLab/Niben261_genome.fasta > ../genomes/chnVSjapVSauVSusa.fasta

bgzip -@ 4 ../genomes/chnVSjapVSauVSusa.fasta
samtools faidx ../genomes/chnVSjapVSauVSusa.fasta.gz

3.3G chnVSjapVSauVSusa.fasta.gz
2.8M  chnVSjapVSauVSusa.fasta.gz.gzi
854KchnVSjapVSauVSusa.fasta.gz.fai

I found many wfmash parameter settings in this file: https://github.com/nf-core/pangenome/blob/master/conf/modules.config . Do you see any problems with them?

Furthermore, the pipeline provides mane wfmash parameters to be set ( https://nf-co.re/pangenome/1.0.0/parameters#wfmash-options ).

I already notified the developer of the Nextflow pipeline ( nf-core/pangenome#168 ).

Thank you in advance for your help,

Michal