Merquryfk bug

[muffato]

Description of the bug

Taking /lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella (/lustre/scratch124/tol/projects/darwin/data/insects/Ypsolopha_sequella) as an example, and using the database genomic_data/ilYpsSequ2/pacbio/kmer/k31/ilYpsSequ2.k31.ktab

• completeness of assembly/release/ilYpsSequ2.1/insdc/GCA_934047225.1.fasta.gz:

  Assembly        Region  Found   Total   % Covered
  ilYpsSequ2.1.GCA_934047225.1    all     659008770       659016853       100.00
  

• completeness of assembly/release/ilYpsSequ2.1_alternate_haplotype/insdc/GCA_934041175.1.fasta.gz:

  Assembly        Region  Found   Total   % Covered
  ilYpsSequ2.1_alternate_haplotype.GCA_934041175.1        all     659008726       659016853       100.00
  

• expected completeness, which can be seen if passing both Fasta files to merquryfk:

  Assembly        Region  Found   Total   % Covered
  ilYpsSequ2.1.GCA_934047225.1    all     524725644       659016853       79.62
  ilYpsSequ2.1_alternate_haplotype.GCA_934041175.1        all     513343328       659016853       77.90
  both    all     644539455       659016853       97.80
  

The bug is in merquryfk, not in the pipeline itself, but until it's solved, the completeness value may not be trusted.

Command used and terminal output

In a directory, create symbolic links to:

• /lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella/genomic_data/ilYpsSequ2/pacbio/kmer/k31/ilYpsSequ2.{hist,ktab}
• /lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella/genomic_data/ilYpsSequ2/pacbio/kmer/k31/.ilYpsSequ2.ktab.*
• /lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella/assembly/release/ilYpsSequ2.1/insdc/GCA_934047225.1.fasta.gz
• /lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella/assembly/release/ilYpsSequ2.1_alternate_haplotype/insdc/GCA_934041175.1.fasta.gz

The command is then:

bsub -M24000 -R"select[mem>24000] rusage[mem=24000] span[hosts=1]" -n 6 -q yesterday -Is \
singularity exec --no-home --pid -B /lustre /nfs/treeoflife-01/teams/shared/nextflow/cache/nxf_singularity/quay.io-sanger-tol-fastk-1.0.1-c1.img \
MerquryFK -P. -T6 $PWD/ilYpsSequ2.k31.ktab \
$PWD/ilYpsSequ2.1.GCA_934047225.1.fasta  $PWD/principal

or

(...)
$PWD/ilYpsSequ2.1_alternate_haplotype.GCA_934041175.1.fasta.gz $PWD/alternate

or

(...)
$PWD/ilYpsSequ2.1.GCA_934047225.1.fasta  $PWD/ilYpsSequ2.1_alternate_haplotype.GCA_934041175.1.fasta.gz $PWD/both

Relevant files

No response

System information

No response

[muffato]

A workaround is to alter the MerquryFK command line to pass the input Fasta twice.

Assembly        Region  Found   Total   % Covered
ilYpsSequ2.1.GCA_934047225.1    all     524725644       659016853       79.62
ilYpsSequ2.1.GCA_934047225.1    all     524725644       659016853       79.62
both    all     524725644       659016853       79.62

[tkchafin]

Do we want this fixed in 2.1.0? I could patch the module this afternoon, otherwise there's nothing else we are currently waiting on for that release

[tkchafin]

Logging for posterity that in 2.1.0 we will remove the completeness metric