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speciationgenomics / scripts

Scripts for analysis used during the course
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fsc-selectbestrun #9

Closed smallfishcui closed 3 years ago

smallfishcui commented 4 years ago

Hi,

Thanks for the course material. Although I m not able to attend the course on site, I have learnt lots of skills here! The procedure with fastsimcoal has been running fine before, but I just lately encountered this error when using ./fsc-selectbestrun.sh "no .bestlhoods file found in run1 ./fsc-selectbestrun.sh: line 37: [: -gt: unary operator expected no .bestlhoods file found in run10 ./fsc-selectbestrun.sh: line 37: [: -gt: unary operator expected no .bestlhoods file found in run100 ./fsc-selectbestrun.sh: line 37: [: -gt: unary operator expected no .bestlhoods file found in run11 " It seems to have an easy fix, however I m not an advanced linux user, can you help with that? Thanks a lot! Cui

joanam commented 3 years ago

Hi Cui, I am glad you find the course information useful. Maybe you have figured it out by now. But this script requires a specific folder structure with different runs in folders called run1, run2 etc. In each such folder, it expects to find a subfolder with the model name (generated by fsc) which contains a bestlhoods file. If you have a different folder structure, the selectbestrun.sh script may fail. I hope that helps. Best, Joana