Hello, I am repeatedly getting the below error running samtools (v1.10) and python (v3.7, though I get the same error when I re-run with python v2.7). I do not believe the error has to do with my SAM-format output, original sample or query reference, as I have switched all out. I found some similar error messages online, but no resolution. Thanks in advance for any possible help.
Command: samtools mpileup -Q 20 -q 5 -d 5000 -uf Ggal_exon_sequences.fasta Mapped_AG_WGS_Ggal_exon.bam | bcftools call -c | vcfutils.pl vcf2fq -d 5 -Q 20 -l 1 >Consensus_AG_WGS_Ggal_exon.fq Error: Use of uninitialized value $l in numeric lt (<) at /usr/local/apps/samtools/1.10/bin/vcfutils.pl line 566, <> line 412. -- Noor D. White, PhD Postdoctoral Fellow, National Science Foundation Postdoctoral Fellow, National Eye Institute, National Institutes of Health Research Collaborator, National Museum of Natural History, Smithsonian Institution NNRL<https://nei.nih.gov/research/research-labs-and-branches/neurobiology-neurodegeneration-repair-laboratory>, National Eye Institute<https://nei.nih.gov/>, NIH<https://www.nih.gov/> 6 Center Dr. Bethesda, MD 20892 (301) 402-5734 www.noorwhite.com<http://www.noorwhite.com/>
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