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sanger-pathogens / Bio-Tradis

A set of tools to analyse the output from TraDIS analyses
https://sanger-pathogens.github.io/Bio-Tradis/
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Error in step 3.5 of bacteria_tradis, using samtools 1.3 #63

Closed juanu closed 8 years ago

juanu commented 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.)

andrewjpage commented 8 years ago

Support has just been added to allow for the samtools 1.3 syntax changes. Thanks for submitting the bug report