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hangelwen / miR-PREFeR

microRNA PREdiction From small RNA-seq data
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During pipeline sam2bam #5

Open Juliix opened 4 years ago

Juliix commented 4 years ago

Hello,

I am trying to run the command pipeline and I have this error after the "Done sam2bam"

I have this error : Error occurred when filtering regions and sorting the BAM file

Did someone has this problem before ? How can I fix it ?

Thank you !

VDaric commented 4 years ago

This is due to a bug in 0.24 miR_PREFeR.py script.

Lines 706 and 707 in miR_PREFeR.py should probably be something like:

command2 = "samtools sort "+ bamfile + " -o " + outbamprefix + ".sort.bam" command3 = "samtools index " + outbamprefix + ".sort.bam"

instead of :

command2 = "samtools sort "+ bamfile + " " + outbamprefix + ".sort" command3 = "samtools index " + outbamprefix + ".sort.bam"