checkm_coverage dropped some bins
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%)
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.