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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
The text was updated successfully, but these errors were encountered:
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.
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
The text was updated successfully, but these errors were encountered: