search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
315 stars 70 forks source link

Curated library option possible bug #324

Closed swomics closed 1 year ago

swomics commented 1 year ago

Hi, thanks for this program. I had interesting results from an earlier version and I'm looking forward to using the new pangenome script with some recent data.

I tried running without a curated library, as the documentation suggests this is optional, however when run without this option panEDTA.sh throws the error:

ERROR: The curated library file is not found or is empty

I got around this by commenting out line 76. Is this ok, or have i made a mistake?

The command I used is this, and the installation was from conda

panEDTA.sh -g genome.list -c merged.transcripts.fa -t 60

oushujun commented 1 year ago

@swomics THank you for reporting. Commenting Line 76 out should be fine. I have improved the parameter reading and should allow you to use no curated library now.