take help from Gallaxy

https://usegalaxy.org/

Hi Julie Mallet . You can try using another tool. Usually, I use samtools for sort and convert sam files in bam files. Maybe it can works for you.

Exemple:

# Converting SAM to BAM:

samtools view -bS My_file.sam > My_file.bam

# Sorting BAM file:

samtools sort My_file.bam > My_file.sorted

I know samtools, and the pipeline was using it. But i fixed my problem, thank you for your answer.

The fix : https://github.com/hangelwen/miR-PREFeR/issues/5