samtools mpileup error - 1 samples in 1 input files
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2.5 years ago

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 • 1.1k views
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pileup] 1 samples in 1 input files

this is just an info/log/warning

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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

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it depends of the size of the input file.

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