Entering edit mode
15 months ago
joseph.kelly.94 ▴ 10
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?
this is just an info/log/warning
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
it depends of the size of the input file.