losing reads from input bam

[flokraft85]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v.2.4.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run wf-human-variation --bam input.bam --sample_name 12345 --out_dir out_folder --ref ref.fa --snp --sv --cnv --str --mod --annotation true --phased --tr_bed /data/ref/human_GRCh38_no_alt_analysis_set.trf.bed --GVCF -profile standard -w /work/ --ubam_map_threads 80

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Hi,
I realized, that some of the reads are getting lost when comparing the input bam, which comes directly from MinKNOW/dorado to the final haplotagged cram generated by the wf-human-variation workflow. I know, there were some issues with unmapped reads. However, the number of unmapped reads is smaller than the number of missing reads. So I wonder, what reads are missing in the wf-human-variation final cram and it is save to only store this.

Best,
FLorian

Relevant log output

n/a

Application activity log entry

n/a

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

dorado_bam	wf-human_variation bam	umapped_bam
raw total sequences:	11234986,00	10961928,00	116969,00
filtered sequences:	0,00	0,00	0,00
sequences:	11234986,00	10961928,00	116969,00
is sorted:	1,00	1,00	1,00
1st fragments:	11234986,00	10961928,00	116969,00
last fragments:	0,00	0,00	0,00
reads mapped:	11118017,00	10961928,00	0,00
reads mapped and paired:	0,00	0,00	0,00
reads unmapped:	116969,00	0,00	116969,00
reads properly paired:	0,00	0,00	0,00
reads paired:	0,00	0,00	0,00
reads duplicated:	0,00	0,00	0,00
reads MQ0:	33337,00	27584,00	0,00
reads QC failed:	0,00	0,00	0,00
non-primary alignments:	3557851,00	3137511,00	0,00
supplementary alignments:	1236500,00	1187730,00	0,00