Cannot write to --joblog error with blech_emg_jetstream_parallel.sh

[natashakbt]

Hello again... I encountered an error while running blech_emg_jetstream_parallel.sh

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parallel: Error: Cannot write to --joblog /media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/results.log.

I did get a message I had never seen before in the previous step of the pipeline emg_local_BSA.py:

Processing : /media/natasha/drive2/Natasha_Data/YW8/YW8_test2_4tastets_240509_135126/
blech_emg_dir: /home/natasha/Desktop/blech_clust/emg
blech_clust_dir: /home/natasha/Desktop/blech_clust

=== EMG params file not found. ===
==> Please copy [[ blech_clust/params/_templates/emg_params.json ]] to [[ blech_clust/params/emg_params.json ]] and update as needed.

I copied the file as instructed and it allowed me to run emg_local_BSA.py. Unsure if that error has any relation to the current one.

[abuzarmahmood]

It sounds like parallel might not have permission to write to that file. Could you try the code below and paste the output here? That will tell us about permissions ls -l /media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/

Alternatively, you could just delete the line below from blech_emg_jetstream_parallel.sh and run again --joblog /media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/results.log

[natashakbt]

Here is the output of ls -l /media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/: ls: cannot access '/media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/': No such file or directory I can also confirm that there are no folders in emg_output, just the file emg_data_readme.txt

blech_emg_jetstream_parallel.sh only has one line of code: parallel -k -j 7 --noswap --load 100% --progress --ungroup --joblog /media/natasha/drive2/Natasha_Data/NB35/NB35_test2_4tastes_240203_135451/emg_output/emgad/results.log bash blech_emg_jetstream_parallel1.sh ::: {1..116}

Should I delete the entire line or just portion you indicated, as below? parallel -k -j 7 --noswap --load 100% --progress --ungroup bash blech_emg_jetstream_parallel1.sh ::: {1..116}

[abuzarmahmood]

For reference, this issue is in commit e9a5857

[abuzarmahmood]

Sorry for the back and forth. It seems like while moving to this commit fixed earlier issues, it itself is part of a chain of partial changes where some of the files were updated but not all of them (hence us encountering errors in subsequent steps). I think we might have to go back to your original commit from issue #158 (commit https://github.com/abuzarmahmood/blech_clust/commit/ab2835e9db5a51a8a6e6e1c7525eebbe087e4bd9), and make a one-time edit for your specific issue. Let's setup a time to do that. I'll send you an email to coordinate