Error with pipeline

[wodanaz]

Hi @johnbradley , I started analyzing the new data after updating the current repo and obtaining the following error:

ERROR: Genome index/dictionary not found.

It also happened when I run:

./run-escape-variants.sh -g NC_045512.fasta ERROR: Genome index/dictionary not found. To fix run ./setup-escape-variants.sh

Thanks!

[johnbradley]

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?

[wodanaz]

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

[johnbradley]

Have you created the picard index file as well? https://github.com/wodanaz/Assembling_viruses/blob/1d0ac3dc9b800894f4b4406852b8086dd7d64057/scripts/create-picard-dictionary.sh#L16-L17

[wodanaz]

i did

[johnbradley]

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

[wodanaz]

Yep, it is working now.

Thanks so much