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grenaud / schmutzi

Maximum a posteriori estimate of contamination for ancient samples
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schmutzi.pl failing on line 372 on some BAMs and not others #26

Open lnpott9 opened 3 days ago

lnpott9 commented 3 days ago

Hello! I have been having some problems using schmutzi when using rescaled BAM files vs just deduplicated BAM files (identical in terms of other processing steps like adapter trimming, merging, mapping, etc). I do not get any errors using the deduplicated BAM files, but I do get errors for all but 2 of the files when I use rescaled files (rescaled using mapDamage2). This is an example of the error message:

programs/schmutzi/src/approxDist.R 55mt_schmutzi_npred_1_split_endo.size.gz > 55mt_schmutzi_npred_2_split_endo.size.param failed: 256 at /programs/schmutzi/src/schmutzi.pl line 372.

Is this an issue with the input BAM files themselves or likely another problem?

grenaud commented 2 days ago

Hello! can you try running the script in R yourself? This could be a missing library issue.