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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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Installation and launch #8

Closed jfong1123 closed 7 years ago

jfong1123 commented 7 years ago

Hello,

I tried installing RetroSeq and launching today. On my path, I have exonerate,bedtools,and samtools-0.1.18.

When I ran the command "perl retroseq.pl" I got the following error:

Nested quantifiers in regex; marked by <-- HERE in m/^[0-9]{2}+ <-- HERE S/ at ../RetroSeq/Utilities.pm line 190. Compilation failed in require at retroseq.pl line 28. BEGIN failed--compilation aborted at retroseq.pl line 28.

If relevant, I am using a Linux cluster (redHat5) with perl version 5.8.8 ("built for x86_64-linux-thread-multi"). Any help would be appreciated.

Thanks!

jfong1123 commented 7 years ago

It is likely a perl version issue, as I have since been able to run the script.