voila tsv error

[Yu Sun]

Hi there, 

I ran majiq-v3 without problem but encountered the following error when trying to run voila tsv on result from heterogen. I have the error message attached. Any help to resolve this would be greatly appreciated. 

Thank you!

Yu

[San Jewell]

Hello Yu,

As a first item, please note that python3.12 is the officially supported version for majiq release version 3.

I have tried running heterogen TSV on the currently released version of majiq/voila and I've not been able to reproduce this issue yet. However, please note that over the past few months, there have been a lot of bug fixed pushed out due to user feedback, so as a first step I'd recommend trying to reinstall/update your majiq/voila installation and see if that fixes the issue straightaway.

If not, I would ask for a list of commands you used to get to this point in the process, either redacted or sent to me directly, so that I can see if there may be an edge case which leads to the errors.

Let me know if you have a chance.

Thanks,

-San

[Yu Sun]

Thanks San,

Could you please tell me the version information for other dependencies? I'll try to reinstall majiq/voila.

Best,

Yu

[Yu Sun]

Hi San,

I reinstalled majiq and voila with python 3.12 but still got the same error when running voila. I attached all my commands and the error message. 

Thank you!

Best,

Yu

[Yu Sun]

I noticed that majiq-v3 build doesn't generate a sql file for me. It generates a folder called sg.zarr containing folders and files shown in the screenshot. Could this be the problem?

[San Jewell]

Hi Yu,

My mistake, I was actually getting confused between two identical threads on the board. I was able to reproduce the issue which was a problem with the --show-read-counts option. I have patched in a fix and the problem should be resolved. Please reinstall voila and try again when you have a moment. This should only require re-running the voila command, not the rest of the steps.

Thanks,

-San

[Miriam Martínez]

Hi everyone,

in order to not open another ticket and as it is related with voila tsv too, I might have found another bug when voila tsv is run with the --show-per-sample-psi option (when I run it without that option, it runs without problems). The command was:

voila tsv -j 4 -f $path/results_voila/voila_tsv_BD_psipersample.tsv --show-read-counts --show-per-sample-psi --changing-between-group-dpsi 0.10 $path/sg.zarr $path/heterogen.voila $path/grp1.sgc $path/grp2.sgc

I leave the error that pops up attached below:

Traceback (most recent call last):
  File "/lustre/opt/campus/0.4/software/MAJIQ/2.5.0-foss-2024a/lib/python3.12/site-packages/rna_voila/run_voila.py", line 535, in main
    args.func()
  File "/lustre/opt/campus/0.4/software/MAJIQ/2.5.0-foss-2024a/lib/python3.12/site-packages/rna_voila/tsv.py", line 88, in __init__
    HeterogenTsv()
  File "/lustre/opt/campus/0.4/software/MAJIQ/2.5.0-foss-2024a/lib/python3.12/site-packages/rna_voila/tsv.py", line 456, in __init__
    super().__init__(ViewHeterogens)
  File "/lustre/opt/campus/0.4/software/MAJIQ/2.5.0-foss-2024a/lib/python3.12/site-packages/rna_voila/tsv.py", line 124, in __init__
    self.tab_output()
  File "/lustre/opt/campus/0.4/software/MAJIQ/2.5.0-foss-2024a/lib/python3.12/site-packages/rna_voila/tsv.py", line 511, in tab_output
    fieldnames += [f'{exp}_psi' for i in range(len(group_names)) for exp in self._experiment_names[i] ]
                                                                            ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'HeterogenTsv' object has no attribute '_experiment_names'. Did you mean: 'experiment_names'?

If this is an actual bug and it gets fixed, can you let me know if it will be necessary to rerun all the pipeline or just the voila command after updating? Thanks!

Best,

Miriam

[San Jewell]

Hi Miriam, 

I was able to reproduce the error on heterogen mode specifically, which was related to the switch as you mentioned. I have added that switch to new test cases. It is an actual bug and I appreciate you reporting it. The issue was in voila only and only the tsv command will need to be re-run. You can reinstall/update voila via pip when you have a chance to receive the update. 

Thanks, 

-San