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Description
Hi! I am hoping to use Gretel to retrieve haplotypes from a set of BAM files. When I run Gretel, though, I get the following error:
[None]
[NOTE] Loaded 0 breadcrumbs from 0 bread slices.
Traceback (most recent call last):
File "/home/sanna/gretel_Env/bin/gretel", line 8, in <module>
sys.exit(main())
File "/home/sanna/gretel_Env/lib/python3.8/site-packages/gretel/cmd.py", line 78, in main
hansel = util.load_from_bam(ARGS.bam, ARGS.contig, ARGS.start, ARGS.end, VCF_h, n_threads=ARGS.threads, debug_reads=debug_reads, debug_pos=debug_pos, stepper="all" if ARGS.pepper else "samtools")
File "/home/sanna/gretel_Env/lib/python3.8/site-packages/gretel/util.py", line 333, in load_from_bam
hansel.L = int(ceil(float(total_covered_snps.value)/n_reads.value))
ZeroDivisionError: float division by zero
The command I am running is:
gretel set_1_ivartrim_sorted.bam output.vcf.gz "ENA|MN908947|MN908947.3" -s 80 -e 100 --pepper
I tried running it with, and without --pepper, and the same error occurs. I also checked using samtools whether the region I am asking for (80-100) has any coverage at all, and it does.
I was wondering if you could please help me with this? I have uploaded the files I used to run the command in a google drive linked here (BAM file + its index, VCF file + its index):
https://drive.google.com/drive/folders/1elkSfPFIaYOUGeotFB8bY_VwXFjoShAC?usp=share_link
I would appreciate your help!
Cheers,
Sana