samtools mpileup error - 1 samples in 1 input files

1

Entering edit mode

3.0 years ago

joseph.kelly.94 ▴ 10

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,

samtools BAM mpileup SAM • 1.3k views

ADD COMMENT • link updated 6 months ago by Damla • 0 • written 3.0 years ago by joseph.kelly.94 ▴ 10

1

Entering edit mode

pileup] 1 samples in 1 input files

this is just an info/log/warning

ADD REPLY • link 3.0 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

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

ADD REPLY • link 22 months ago by keren.danan ▴ 20

0

Entering edit mode

it depends of the size of the input file.

ADD REPLY • link 22 months ago by Pierre Lindenbaum 164k

0

Entering edit mode

Could you find a solution to your problem?

ADD REPLY • link 6 months ago by Damla • 0

Login before adding your answer.