search

erhard-lab / gedi

GNU General Public License v3.0
2 stars 1 forks source link

Genomic name does not exist in config/genomic #17

Open ericmalekos opened 1 month ago

ericmalekos commented 1 month ago

I am indexing the genome and it runs to completion

gedi -e IndexGenome -s ./genome/GCA_GRCh38_noALT_fusions.fa -a ./genome/annotations/stringtie_fusion.sorted.gtf -nomapping

However when I try to call ORFs the genome cannot be found

gedi -e Price -reads /gstore/scratch/u/malekose/riboseq/stringtie_fusion/merged_Aligned.out.bam -genomic stringtie_fusion.sorted -p
...

Error:
Genomic name stringtie_fusion.sorted does not exisit in config/genomic!

According to these instructions there should be an oml file created in $HOME/.gedi/genomic, but that is not the case for me:

ls -lah $HOME/.gedi/
drwxr-xr-x  2 malekose idmgmt 8.0K Aug  7 09:06 .
drwx------ 21 malekose idmgmt 8.0K Aug  6 16:59 ..
-rw-r--r--  1 malekose idmgmt 2.6K Aug  7 09:06 gedi0.log

What can I do, I have tried specifying the full path to the index, but nothing seems to work.