Skip to content

Issue with --correctErr BOOL:Perform error correction for input reads (default: True) #12

@DerekLake

Description

@DerekLake

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions