Mandalorion-old icon indicating copy to clipboard operation
Mandalorion-old copied to clipboard

Published 20 hours ago • verified publisher icon christopher-vollmers

Error finding GMAP index

Open ghost opened this issue 6 years ago • 0 comments

When running Mandalorion with the following command:

python3 Mandalorion_just_align.py -f /data/csijcs/nanopore/WW_Nanopore_K562_107/basecalls/workspace/all/WW_Nanopore_K562_107_all_pass.fastq -g /data/csijcs/nanopore/GRCh38/GRCh38 -q 2 -t 64

I keep getting this issue:

Unable to find genome directory /usr/local/share//data/csijcs/nanopore/GRCh38. Either recompile the GMAP package

I have recompiled and keep getting the same error. I'm not sure why it is looking in /usr/local/share/. I even tried to recompile GMAP without specifying a directory (-D) and by default it goes to /home/csijcs/anaconda3/share/GRCh38. I tried running Mandalorion with that path and got the same error. Can anyone help?

ghost avatar Apr 10 '18 10:04 ghost