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HaploKit / Strainline

Full-length de novo viral haplotype reconstruction from noisy long reads
GNU General Public License v3.0
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Issue with --correctErr BOOL:Perform error correction for input reads (default: True) #12

Open DerekLake opened 1 year ago

DerekLake commented 1 year ago

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

SixEl27 commented 6 months 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.