Closed juanu closed 8 years ago
When using samtools 1.3, there is an error in step 3.5 of the bacteria_tradis pipeline. The error is:
..........Step 3.5: Convert output from SAM to BAM and sort [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
This seems to be due to changes in the samtools options (https://github.com/samtools/samtools/releases/tag/1.3):
obsolete samtools sort in.bam out.prefix usage has been removed. If you are still using ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead. (#295, #349, #356, #418, PR #441; see also discussions in #171, #213.)
Support has just been added to allow for the samtools 1.3 syntax changes. Thanks for submitting the bug report
When using samtools 1.3, there is an error in step 3.5 of the bacteria_tradis pipeline. The error is:
This seems to be due to changes in the samtools options (https://github.com/samtools/samtools/releases/tag/1.3):