checkm_coverage dropped some bins

[emilyjunkins]

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%)