low_confidence.bed empty file

[agolicz]

Hi, Thanks very much for the great tool. We've been trying CRAQ out in several of our assembly projects and we sometimes run into strange behavior where analysis seems to finish ok, but low_confidence.bed is empty and the Low-confident.Rate in out_final.Report is 0. We know for sure that is not the case (from quality scores) and as a parallel run on a different machine gave >100 low confidence points. The fasta file after breaks is also not produced. Would there be a chance to look into it? It is a 1.1Gb genome and we are using a 500Gb mem, 28 CPU machine, so resources should be plenty.

Running CRAQ analysis .........
PARAMETERS:
Genome sequence(-g): yahs.out_scaffolds_final.fa
SMS input(-sms): lr.fq.gz
NGS input(-ngs): SRR10382366_1.fastq  SRR10382366_2.fastq
Minimum NGS clipped-reads (-sn): 2
Minimum SMS clipped-reads (-ln): 2
NGS clipping coverRate(-sf): 0.75
SMS clipping coverRate(-lf): 0.75
Lower clipping rate for heterozygous allele(-hmin): 0.4
Upper clipping rate for heterozygous allele(-hmax): 0.6
Block score benchmarking (-rw): 500000
Gap[N] is treated with (-gm): 1:CRE
Minimum gapsize(-mgs): 10
Break chimera fragments (-b): T
Search error region (-ser): T
Mapping SMS reads use (-x): map-hifi
Mapping quality (-q): 20
Window size for error normalizing (-nw): 103347
Plot CRAQ metrics (-pl): F
Alignment thread(-t): 24
Current working at : /vol/volume/agolicz/napus_microc/noUL/stringent3
CRAQ output dir(-D): /vol/volume/agolicz/napus_microc/noUL/stringent3/output
-------------------------Start Running-------------------------
Running NGS short-reads CRAQ analysis ......
CMD: /vol/volume/agolicz/CRAQ/bin/../src/runSR.sh -g yahs.out_scaffolds_final.fa  -z seq.size -1  SRR10382366_1.fastq -2 SRR10382366_2.fastq -q 20 -m 2 -f 0.4 -h 0.6 -r 0.75 -a 20 -t 24
worker_pipeline::
worker_pipeline:: NGS reads aligning and filtering
[M::worker_pipeline:: Sort bamfiles]
[M::worker_pipeline:: Compute effective NGS coverage]
[M::worker_pipeline:: Collect potential CRE|RH]
SR clipping analysis completed. Check current directory SRout for final results!

Running CRAQ benchmark analysis ......
CMD: /vol/volume/agolicz/CRAQ/bin/../src/runAQI_NGS.sh -g  yahs.out_scaffolds_final.fa  -z seq.size   -e SRout/SR_eff.size  -c SRout/SR_putative.RE.RH  -d SRout/SR_sort.depth  -r 0.75 -p 0.4 -q 0.6  -n 10 -s 103347 -w 500000    -j 1 -u T -v F -y F -x /vol/volume/agolicz/napus_microc/noUL/stringent3/output/seq.size
[M::worker_pipeline:: Collect potential CRE|H]
[M::worker_pipeline:: Get putative CRE]
[M::worker_pipeline:: Search noisy region]
[M::worker_pipeline:: Quality benchmarking]
[M::worker_pipeline:: Create regional metrics]
[M::worker_pipeline:: Create final report]
CRAQ analysis is finished. Check current directory runAQI_out for final results!