Running STACKS 2.0b using populations with only one group in each population

[Shane]

Hi,

I am trying to run STACKS using four samples.

Each of them are in different species, so I wrote them as their own species in the population map.

But when I tried to run STACKS, it gave me an error stating that:

Parsed population map: 4 files in 4 populations and 1 group.

Error: Failed to open '/gpfs1m/projects/landcare00051/phd/data/sub_fasta/sam/bam/AXX.bam'.

This is the command I used to run STACKS:

ref_map.pl -T 10 --samples /gpfs1m/projects/landcare00051/phd/data/sub_fasta/sam/bam/ --popmap /gpfs1m/projects/landcare00051/phd/data/sub_fasta/stacks/popmap.txt -o /gpfs1m/projects/landcare00051/phd/data/sub_fasta/stacks/data/ -X "populations: --fstats --vcf --vcf_haplotypes --structure --phylip -O /gpfs1m/projects/landcare00051/phd/data/sub_fasta/stacks/results/"

Sorry if I am missing something simple, but could you help me what might be the problem is?

Kind regards,

Shane

[Julian Catchen]

Hi Shane,

The program seems to have read your population map without a problem. It
is looking at each sample listed in the population map and looking for a
BAM file, based on the sample name in the --samples directory, but it is
not finding the properly named sample. Review your --samples path and
make sure your sample names correspond to the sorted BAM files names.

julian



Shane wrote on 8/15/18 2:19 PM:

[Shane]

Hi Julian,

Yes there was a typo... Sorry I didn't see this sooner.

Thank you so much for your help!

Kind regards,

Shane

2018년 8월 16일 목요일 오전 11시 20분 33초 UTC+12, Julian Catchen 님의 말: