Missing PercentContam in cgMLST mode
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gputzel commented
I am trying to run ConFindr in the (experimental) cgMLST mode, using a subset of a Staphylococcus aureus cgMLST scheme downloaded from https://www.cgmlst.org/ncs (and formatted as described in the ConFindr documentation).
The command I tried:
confindr -fid .R1. -rid .R2. -i fastq_files/ -o output_dir -t 4 -Xmx 10g --verbosity debug --keep_files -cgmlst cgmlst_subset.fasta
The stdout is then:
2023-12-11 11:41:29 Welcome to ConFindr 0.8.1! Beginning analysis of your samples...
2023-12-11 11:41:29 Beginning analysis of sample sampleName...
2023-12-11 11:41:29 Sample is paired. Sample name is sampleName
2023-12-11 11:41:29 Checking for cross-species contamination...
2023-12-11 11:41:46 Extracting conserved core genes...
2023-12-11 11:42:05 Quality trimming...
2023-12-11 11:43:40 Detecting contamination...
2023-12-11 11:43:40 Since this is the first time you are using this database, it needs to be indexed by KMA. This might take a while
2023-12-11 11:44:10 Total gene length is 1633944
2023-12-11 13:43:45 Done! Number of contaminating SNVs found: 166
2023-12-11 13:43:49 Contamination detection complete!
And the contents of confindr_report.csv are:
Sample,Genus,NumContamSNVs,ContamStatus,BasesExamined,DatabaseDownloadDate
sampleName,Staphylococcus,166,True,1633944,2021-4-29
Notably missing from the output is the estimate of percent contamination (PercentContam) that I am used to seeing.
Some details:
ConFindr version 0.8.1 from bioconda.
KMA version 1.4.9