canthonyscott
commented
3 years ago This is not so much a bug as just a feature not presently implemented. Currently the software does not operate on chromosome scaffolds with names such as "NW_018395390.1". The best course of action would be to filter those out and keep only the full chromosomes such as chr1, chr2, etc.
Describe the bug There appears to be an issue with the chromosome entry. I am trying to calculate coverage for an organism with a genome at scaffold level of assembly.
To Reproduce clubcpg-coverage -a P_bismark_bt2_sorted.deduplicated.bam -o ${PWD} --bin_size 100 -chr NW_018395390.1 --no_overlap False
Error message Log file: /media/kevlab/projects/helicoverpa_epigenetics/exp/wgbs/analysis/20200817/barcode_analysis/CompleteBins.P_bismark_bt2_sorted.deduplicated.bam.NW_018395390.1.log Traceback (most recent call last): File "/media/kevlab/projects/helicoverpa_epigenetics/exp/wgbs/analysis/20200817/barcode_analysis/clubcpg/bin/clubcpg-coverage", line 98, in
output_file = calc.analyze_bins(chrom_of_interest)
File "/media/kevlab/projects/helicoverpa_epigenetics/exp/wgbs/analysis/20200817/barcode_analysis/clubcpg/lib/python3.6/site-packages/clubcpg/CalculateBinCoverage.py", line 148, in analyze_bins
new[individual_chrom] = chromosome_lengths[individual_chrom]
KeyError: 'NW_018395390.1'
Expected behavior An output file containing coverage estimates across the specified bins for the chromosome/scaffold of interest.
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