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medvir / SmaltAlign

Quick iterative alignment of reads against a given reference using smalt.
MIT License
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=-=-= lofreq with 0 cores =-=-= #7

Closed Masterxilo closed 1 year ago

Masterxilo commented 3 years ago

Hi there,

I am building a docker container for this pipeline. For testing, I am running it on a machine with just 1 core, but I have to remove this one line of smaltalign.sh: cores=$(expr $cores / 2) ### only run on half the cores

Because otherwise it outputs '=-=-= lofreq with 0 cores =-=-=' and produces a bunch of failures and division by 0 errors...

Can you change it so that if cores is 0 it at least sets it to 1? For example with another line:

cores="${cores/0/1}"

cheers Paul

MaryamZaheri commented 3 years ago

Dear Paul, Thank you very much for your comment. It is modified in the coded.