Error: Could not open the input file

Question

[taniamahmood38]

Dear all,

I am using pool-HMM tool to estimate allele frequencies and detect selective sweeps in my pooled-seq data. The input data is required in pileup format using samtools which i have with me. Now, when i run the command

python2 pool-hmm.py --prefix sample_pileup -n 30 -c 3 -C 50 -e sanger -t 0.005 -o > output

It returns with an error

Could not open input file sample_pileup

I do not understand what is the issue. I have the input file in my path as well. Kindly help me out in resolving this issue. Any help would be highly appreciated.

Thanks in advance

[seidel]

Have you tried -f sample_pileup? The docs seem to suggest that using the --prefix implies that the file ends with a suffix of .pileup, but your file does not have this suffix. If you type ls -l sample_pileup, do you get information about your file (just to confirm the file is in your environment the way you think it is)?

[taniamahmood38]

Thank you for pointing in right direction. I resolved the issue. First thing is to end the file with a suffix of .pileup, as you suggested. Secondly, -f requires just the prefix of the input file not the full input file name. In my case, now the correct command is :

./pool-hmm.py --prefix sample -n 30 -c 3 -C 50 -e sanger -t 0.005 -o > output

Where sample.pileup was my input file and I just used the prefix sample in my command.