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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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error in README #2

Open jlrf98 opened 9 years ago

jlrf98 commented 9 years ago

Dear lh3, I am trying to run the command as described in the README to produce the .diploid.fq.gz file. I have the latest (1.2 htslib) samtools/bcftools/vcfutils.pl

samtools mpileup -C 50 -u -f /data/Databases/human_g1k_v37.fasta NA12878.GRCh37.ILLUMINA.bwa.CEU.high_coverage.20100311.bam | /usr/local/bin/bcftools view -c - | /usr/local/bin/vcfutils.pl vcf2fq -d 10 -D 100 | gzip > NA12878.GRCh37.ILLUMINA.bwa.CEU.high_coverage.20100311.bam.diploid.fq.gz

The error I get is Error: Could not parse --min-ac - [E::hts_open] fail to open file 'NA12878.GRCh37.ILLUMINA.bwa.CEU.high_coverage.20100311.bam' [mpileup] failed to open NA12878.GRCh37.ILLUMINA.bwa.CEU.high_coverage.20100311.bam: No such file or directory Use of uninitialized value in length at /usr/local/bin/vcfutils.pl line 565. Use of uninitialized value in length at /usr/local/bin/vcfutils.pl line 565.

Looking at the manual, the "-c " parameter has changed across versions. What is the updated command?

Thanks, Juan

lh3 commented 9 years ago

You need to use samtools-0.1.x. Samtools-1.x does not work. I will leave this issue open until I update README.