-
Notifications
You must be signed in to change notification settings - Fork 66
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
[CLI] sz_split error #139
Comments
That's interesting, @lborcard, thank you for submitting the issue! |
thank your answer, yes I can give you an example file. here is an example: https://s3.amazonaws.com/nanopore-human-wgs/bulkfile/GXB02001_20230509_1250_FAW79338_X3_sequencing_run_NA12878_B1_19382aa5_ef4362cd.fast5 I will try to split and see if I run into the same error. thanks for your reply edit: the error is reproducible with the file posted
|
I am pretty sure that the python split.py does not work with the |
@lborcard The split works for me. Can you provide details on your machine? OS ? |
We should perhaps use logging.exception or traceback. The error message above just prints the X0 filename - likely due to running out of disk space? Looking at the code its not obvious what possible exception was thrown with the filename as the message. https://stackoverflow.com/questions/1483429/how-do-i-print-an-exception-in-python |
@MarkReedZ sounds reasonable. |
|
I tested again today after updating to 3.84 and I get the same error message |
Hi @lborcard! I've just tried using it with v3.9 and it works fine. Please let me know if the issue persists. |
Thank you very much for sharing this great project.
I am using the cli tool sz_split and it's stopping after the first split when I specify
-n 20
.It produces only 1 of the 20 files and stops with this error message:
I am splitting a .fast5 (hdf5 files for sequencing data).
sz_split -n 20 gxb03325_20240327_1204_FAX92537_X5_sequencing_run_no_sample_ac8a3c2b_b3c8a5e7.fast5
best,
Loïc
The text was updated successfully, but these errors were encountered: