Issue with refineinsertions.sh

schatzlab / crossstitch

Code for phasing SVs with SNPs

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Issue with refineinsertions.sh #7

Closed CWYuan08 closed 5 years ago

CWYuan08 commented 5 years ago

Hi there, I am now running crossstitch on my laptop and I tried refineinsertions.sh. However, I got this: readlink: illegal option -- f usage: readlink [-n] [file ...] usage: dirname path

The command I used: ./refineinsertions.sh raw.vcf Sorted.bam ref.fa outfile How to use command this properly? Thank you very much

mschatz commented 5 years ago

Im guessing you are trying to run on mac, which uses different options for readlink than a linux machine. Unfortunately, only linux is supported at this time

Good luck Mike