Issue with isONform

[molbioinformatics]

Hi, I am trying to run isONform (version 0.2.0). I manually ran pychopper, isONclust and then isONcorrect (run_isoncorrect --t 12 --fastq_folder isONclust/fastq_files/ --outfolder isONcorrect/correction/ ). I can see that isONcorrect created "corrected_reads.fastq" fastq files in numbered subfolders in the isONcorrect/correction/ folder. Then I ran isoONform using:
isONform_parallel.py --fastq_folder ./isONcorrect/correction/ --outfolder ./isONform/ --split_wrt_batches --t 40. However it spits out an error:
**Running isONform batch_id:157828.0... creating ./isONform/168235
Running isONform batch_id:168235.0... creating ./isONform/268243
Running isONform batch_id:268243.0... creating ./isONform/146478
Running isONform batch_id:146478.0... multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/user/miniconda3/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/user/miniconda3/bin/isONform_parallel.py", line 51, in isONform
subprocess.check_call(
File "/home/user/miniconda3/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['python', '/home/user/miniconda3/bin/main.py', '--fastq', '/tmp/tmpcivcbzwz/split_in_batches/157828_0.fastq', '--outfolder', './isONform/157828', '--exact_instance_limit', '50', '--k', '20', '--w', '31', '--xmin', '18', '--xmax', '80', '--delta_len', '5', '--exact', '--parallel', 'True', '--delta_iso_len_3', '30', '--delta_iso_len_5', '50']' returned non-zero exit status 2.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/user/miniconda3/bin/isONform_parallel.py", line 354, in
main(args)
File "/home/user/miniconda3/bin/isONform_parallel.py", line 283, in main
for x in pool.imap_unordered(isONform, instances):
File "/home/user/miniconda3/lib/python3.9/multiprocessing/pool.py", line 870, in next
raise value
subprocess.CalledProcessError: Command '['python', '/home/user/miniconda3/bin/main.py', '--fastq', '/tmp/tmpcivcbzwz/split_in_batches/157828_0.fastq', '--outfolder', './isONform/157828', '--exact_instance_limit', '50', '--k', '20', '--w', '31', '--xmin', '18', '--xmax', '80', '--delta_len', '5', '--exact', '--parallel', 'True', '--delta_iso_len_3', '30', '--delta_iso_len_5', '50']' returned non-zero exit status 2.**
Please let me know how can I fix this. Thanks.

[aljpetri]

Hello,
thank you for reporting the error. I have added a new release for isONform (v0.3.0) that hopefully fixes the problem.
If the error persists, I, however, would require additional information from you to find the source.
Could you then please send me the contents of the stdout and stderr files for the instance located in ./isONform/157828?
Best,
Alex

[aljpetri]

Hi,
does the error still persist or did the new release fix the problem?
Best regards,
Alex

[alexyfyf]

I'm having the same issue with v 0.3.1
I have looked at the stderr in the corresponding isonform folder, and the message is this:

python: can't open file '/vast/projects/lab_davidson/yan.a/conda_env/isoncorrect/bin/main.py': [Errno 2] No such file or directory

I installed the isonclust, isoncorrect, isonform with pip in a conda environment (python 3.10.8). suspect it's related to conda/python, but would appreciate if you could have a look.

[GGSonoda]

I'm having the same issue with v 0.3.1 I have looked at the stderr in the corresponding isonform folder, and the message is this:

python: can't open file '/vast/projects/lab_davidson/yan.a/conda_env/isoncorrect/bin/main.py': [Errno 2] No such file or directory

I installed the isonclust, isoncorrect, isonform with pip in a conda environment (python 3.10.8). suspect it's related to conda/python, but would appreciate if you could have a look.

So, I'm not a dev, but for now, I was able to fix that error by manually adding the main.py file (I downloaded from this git) to the isONform path. Maybe it will work for you as a temporary solution.

best,

[aljpetri]

Hi thank you very much for reporting the error. I realized that the main.py was missing in the release uploaded to pypi.
I have yanked the broken release now and uploaded a new release version '0.3.2,', for which the main.py is properly contained in the release.

[alexyfyf]

Hi thank you very much for reporting the error. I realized that the main.py was missing in the release uploaded to pypi. I have yanked the broken release now and uploaded a new release version '0.3.2,', for which the main.py is properly contained in the release.

Hi @aljpetri the new version works well. Just one small thing I noticed, the isonform did not work with relative path, not sure if this is something you could improve, but I just provided it with an absolute path, and worked it out.

Thank you.
Alex