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checkm_coverage dropped some bins

Open emilyjunkins opened this issue 1 year ago • 1 comments

Hello,

I am running checkm v1.2.1. I ran coverage for my bins but the output seems to drop some of the bins, particularly those that I expect to have high coverage and represent a major portion of each community? Essentially, the coverage table only shows one bin from one sample and not the other two. Am I missing something about how the coverage command works?

checkm coverage --all_reads -x fa bins/ checkm_coverage.tsv allreads_LS01_001_alignment_sorted.bam allreads_LS01_002_alignment_sorted.bam allreads_LS01_024_alignment_sorted.bam

I had roughly these results for each of my bam files:

     # total reads: 10003114
      # properly mapped reads: 4253379 (42.5%)
      # duplicate reads: 0 (0.0%)
      # secondary reads: 3753117 (37.5%)
      # reads failing QC: 470071 (4.7%)
      # reads failing alignment length: 1268846 (12.7%)
      # reads failing edit distance: 257701 (2.6%)
      # reads not properly paired: 0 (0.0%)

emilyjunkins avatar Jan 24 '24 14:01 emilyjunkins

Same thing happening here.

checkm coverage \
    --threads 24 \
    --extension .fasta \
    <somepath>/bins_output \
    <somepath>/checkm_coverage.tsv \
    <somepath>/49_1_L001.bam \
    <somepath>/49_1_L002.bam \
    <somepath>/49_2_L001.bam \
    <somepath>/49_2_L002.bam \
    <somepath>/49_3_L001.bam \
    <somepath>/49_3_L002.bam

checkm lineage_wf works fine on the same directory of bins.

ttubb avatar Jan 16 '25 17:01 ttubb