Error: Could not open the input file
Entering edit mode
2.3 years ago

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 --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

linux samtools pool-HMM • 489 views
Entering edit mode

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)?

Entering edit mode

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 :

./ --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.


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