Failed due to mate not found:

[AlcaArctica]

Hi, I tried to re-implement the workflow but found the following problem:

I downloaded the dataset ERR14654081 and ERR14654084 from you publication (CIFI and HIFI data of the medfly). I constructed an assembly of the medfly with hifiasm as described:

hifiasm \
  -o medfly \
  -t 72 \
  -D 20 \
  -N 200 \
  --h1 cifi_pe_HiC_R1.fastq \
  --h2 cifi_pe_HiC_R2.fastq \
  ERR14654084.fastq.gz

Then I followed the pore-c workflow with the CIFI data and the resulting hifiasm assembly as reference:

nextflow run epi2me-labs/wf-pore-c \
  -work-dir medfly_assembly/work \
  --fastq medfly_assembly/ERR14654081.fastq.gz \
  -c nextflow_slurm.config \
  --ref medfly_assembly/medfly.hic.hap1.p_ctg.fasta \
  --cutter 'HindIII' \
  --out_dir medfly_assembly \
  --threads 72 \
  --minimap2_settings '-x map-pb' \
  --paired_end \
  -profile singularity

Now the problem is that the resulting medfly_assembly/paired_end/ERR14654081.ns.bam file does not seem to contain any valid reads. When filtering it with 2024-sep-mapqfilter/filter_bam the log file reports:

Filtration Statistics:
Total pairs processed: 2120380
Passed pairs: 2000833
Failed due to unmapped: 66343
Failed due to not paired: 64454
Failed due to low MAPQ: 53204
Failed due to mate not found: 14588107

When comparing the file sizes this is confirmed:

15G	ERR14654081.ns.bam
2.6G	ERR14654081.mapq_filtered_paired_end.bam

So mapping statistics are in fact great, but there are so many 'no mate found' reads that of course the subsequent Hi-C contact matrice contains no reads! I also tried to skip the filtering step (in case something is wrong there), but the end result is the same (no reads in contact matrice).

Any idea, what is going on?

Thank you

Datasets:

https://www.ncbi.nlm.nih.gov/sra/ERR14654081
https://www.ncbi.nlm.nih.gov/sra/?term=ERR14654084