Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FileNotFoundError .wig when run --sv #23

Open
Sondr11 opened this issue Jul 23, 2023 · 2 comments
Open

FileNotFoundError .wig when run --sv #23

Sondr11 opened this issue Jul 23, 2023 · 2 comments

Comments

@Sondr11
Copy link

Sondr11 commented Jul 23, 2023

Hi.
I try run TIDDIT.py --sv for file bam of nipt data.
I used command as: python /home/TIDDIT/TIDDIT.py --sv --bam 'file_to_path_bam' --ref 'file_to_path_hg19.fa'
I recieved error below:
'Traceback (most recent call last):
File "/home/TIDDIT/TIDDIT.py", line 91, in
TIDDIT_calling.cluster(args)
File "TIDDIT_calling.py", line 207, in TIDDIT_calling.cluster
coverage_data,span_data=TIDDIT_coverage.coverage(args)
File "TIDDIT_coverage.py", line 8, in TIDDIT_coverage.coverage
for line in open(args.o+".wig"):
FileNotFoundError: [Errno 2] No such file or directory: 'output.wig'

When running, I see it creat two file as: 'output.gc.wig' and 'output.sample.bam'. But I don't see file 'output.wig'
Please help me to fix this problem.
Thank you so much

@J35P312
Copy link
Owner

J35P312 commented Jul 24, 2023

Hello!
Though luck! I notice you are running an old version of TIDDIT. Old TIDDIT consisted of a C++ module as well as python module. I believe the C++ module crashed; could you send more of the output? That error message should have been printed sometime before the missing file error.

Alternatively, you may try to update TIDDIT to a later version.

It is cool that you are running tiddit on NIPT data! Is the data paired-end data? TIDDIT will only work on paired-end data.
New (> 3.0.0) will probably work on single-end but there are better tools designed for that purpose. Usually NIPT data is too shallow for doing a meaningful paired-end analysis, you may be better off using read depth approaches such as WiseCondorX or CNVkit.

Good luck!

@Sondr11
Copy link
Author

Sondr11 commented Aug 1, 2023

Thank you so much

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants