Open DerekLake opened 1 year ago
I've faced the same issue and making a copy of the input fasta file into the output directory and renaming it "corrected.0.fa" seems to do the trick. However, without error correction, the result is not really useful.
Whenever I use the --correctErr option as False, it can not complete haplotyping because "FileNotFoundError: [Errno 2] No such file or directory: 'corrected.0.fa'". This would be a helpful option as ONT's R.10 series flow cell and chemistry purports 99.6% accuracy, and I do not want it "correcting" reads that are already correct possibly. Any help would be very appreciated! Thanks for this great software.
Full slurs output:
Skip Step1, do not perform error correction. Traceback (most recent call last): File "/projects/comp_genomics/dlake/tools/miniconda3/envs/strainline/src/reformat_fa.py", line 29, in
reformat_fasta(in_fa, out_fa)
File "/projects/comp_genomics/dlake/tools/miniconda3/envs/strainline/src/reformat_fa.py", line 8, in reformat_fasta
with open(in_fa) as fr:
FileNotFoundError: [Errno 2] No such file or directory: 'corrected.0.fa'
srun: error: cn73: task 0: Exited with exit code 1