samtools mpileup error - 1 samples in 1 input files

Question

[joseph.kelly.94]

Hi All,

I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered the following command

samtools mpileup  -f /home/path_to_reference/nCoV_Jan31.fa.fasta sorted_sample1.sam > sample.mpileup

The message returned is [mpileup] 1 samples in 1 input files, nothing more is generated from there.

For clarity sake, my bam file has been correctly sorted and indexed. Could anyone offer any suggestions?

Thanks,

[Pierre Lindenbaum]

pileup] 1 samples in 1 input files

this is just an info/log/warning

[keren.danan]

Do you know how much time it is supposed to run if only a warning? It seems I have the same issue and the process won't finish, it runs already more than an hour. Thanks

[Pierre Lindenbaum]

it depends of the size of the input file.