J35P312
commented
1 year ago 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
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_pathhg19.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 TIDDITcoverage.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