"The sequence "chr1" was not found"

[selasphoruskershaw]

Hello,

I'm trying to follow the msmc tutorial to prepare my data for msmc2. However, I am receiving the following error:
"[E::faidx_adjust_position] The sequence "chr1" was not found"

I am using the following command:

samtools mpileup -q 20 -Q 20 -C 50 -u -r chr1 -f ragtag.scaffolds.fasta s2800_chr.bam | bcftools call -c -V indels | ~/Swallows/msmc2/msmc-tools/bamCaller.py 12 out_mask.bed.gz | gzip -c > out.s2800.vcf.gz

I get the following message:
[warning] samtools mpileup option u is functional, but deprecated. Please switch to using bcftools mpileup in future.
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 1 samples in 1 input files

Then the following repeats over and over again:
"[E::faidx_adjust_position] The sequence "chr1" was not found"

If you could please help me get this running I'd greatly appreciate it!

[stschiff]

I think the error message is pretty clear. It seems you're trying to run samtools mpileup queuing a chromosome that doesn't exist in your BAM file.