Closed wodanaz closed 3 years ago
This error is because the script did not find NC_045512.fasta.fai
and/or NC_045512.dict
files that are created by running:
./setup-escape-variants.sh -g NC_045512.fasta
These files should be in the same directory as NC_045512.fasta
- current directory in your case.
Have you run setup-escape-variants.sh on this file already?
It was a new run for setting up the genome index
But I did the index manually and then it also happened when I run:
sbatch --mail-type=END --mail-user=alebesc@gmail.com run-dds-escape-variants.sh -g NC_045512.fasta -d /gpfs/fs1/data/wraycompute/alejo/CoV_data/March_3_data -i Polage_6840_210301A5 -s
Have you created the picard index file as well? https://github.com/wodanaz/Assembling_viruses/blob/1d0ac3dc9b800894f4b4406852b8086dd7d64057/scripts/create-picard-dictionary.sh#L16-L17
i did
Are you running from the /data/wraycompute/alejo/Assembling_viruses
directory on HARDAC?
If so it looks like the NC_045512.fasta.fai
file wasn't created when indexing the genome.
Perhaps this isn't the best file to check.
You could try commenting out these lines to turn this check off:
https://github.com/wodanaz/Assembling_viruses/blob/1d0ac3dc9b800894f4b4406852b8086dd7d64057/run-escape-variants.sh#L91-L97
Yep, it is working now.
Thanks so much
Hi @johnbradley , I started analyzing the new data after updating the current repo and obtaining the following error:
It also happened when I run:
Thanks!