I had an issue running Strainline using its relative path (I just saw it was deprecated in the README.md):
Strainline/src/strainline.sh -i reads.fasta -o out -p ont -t 15
The error message was:
Step1: read error correction. Finished.
python: can't open file '/<abs path to>/out/Strainline/src/reformat_fa.py': [Errno 2] No such file or directory
I think it is because the path to Strainline scripts was computed with basepath=$(dirname $0). I changed it to compute the absolute path to Strainline scripts. It worked for me, I hope it can be useful.
HaploKit
commented
2 years ago
Hi,
I had an issue running Strainline using its relative path (I just saw it was deprecated in the README.md):
The error message was:
I think it is because the path to Strainline scripts was computed with
basepath=$(dirname $0). I changed it to compute the absolute path to Strainline scripts. It worked for me, I hope it can be useful.Best