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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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error --min-ac - #29

Open rgolira opened 3 years ago

rgolira commented 3 years ago

Dear lh3,

I tried to run this command: samtools mpileup -C50 -uf ref.pri_genomic.fna A_41_sorted.bam | bcftools view -c - | vcfutils.pl vcf2fq -d10 -D100 | gzip > A_41_psmc.fq.gz

I tried different commands, but always the following error message appears: Could not parse --min-ac - Use of uninitialized value $l in numeric lt (<) at /opt/apps/software/BCFtools/1.10.2-GCC-8.3.0/bin/vcfutils.pl line 566. Use of uninitialized value $l in numeric lt (<) at /opt/apps/software/BCFtools/1.10.2-GCC-8.3.0/bin/vcfutils.pl line 566.

I used CentOS 7.8.2003 samtools/0.1.19 bcftools/1.10.2 samclip/0.2

I am not sure what else I can do.

Thanks in advance.

Giov12 commented 2 years ago

I am also running into this issue. Were you or anybody else able to figure out a workaround?

llyNINI commented 2 years ago

You can use bcftools call -c，cause you have a higher version bcftools.