Cache entry deserialization failed, entry ignored

[vinitamehlawat]

Hi Authors,

I was able to run TOGA on my couple of species, but somehow, after running for 11 hours, I got this error for one of my species in my sbatch error file.

After loading nextflow module and installing importlib-metadata using pip install importlib-metadata I ran toga with following command

./toga.py /home/vlamba/BD-CG.chain /home/vlamba/CG.bed /home/vlamba/CG.2bit /home/vlamba/BD.2bit -i /home/vlamba/CG-isofrom.txt --project_dir /home/vlamba/BD_gene-loss --kt --cb 10,100 --cjn 500 --ms

Cache entry deserialization failed, entry ignored Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-3HJdri/pip/ You are using pip version 8.1.2, however version 23.3.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-msMJKV/importlib-metadata/ You are using pip version 8.1.2, however version 23.3.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Traceback (most recent call last): File "./toga.py", line 8, in import importlib.metadata as metadata ModuleNotFoundError: No module named 'importlib.metadata'

Here are some last lines from my toga .log file

`Polling iteration 653; already waiting 39180 seconds. Polling iteration 654; already waiting 39240 seconds. Polling iteration 655; already waiting 39300 seconds.

CESAR jobs done

Checking whether all CESAR results are complete 2 CESAR jobs crashed, trying to run again... !!RERUN CESAR JOBS: Pushing 2 jobs into 100 GB queue Selected parallelization strategy: nextflow Parallel manager: pushing job nextflow /scrfs/storage/vlamba/home/TOGA/execute_joblist.nf --joblist /home/vlamba/BD_gene-loss/_cesar_rerun_batch_100 Monitoring CESAR jobs rerun

Stated polling cluster jobs until they done

CESAR jobs done

` I would be grateful if you could suggest any solution for this.

My second concern is running time: my first species took 9hr:40min to complete when I ran TOGA for the first time, the second took 10hr:21min, and the third failed after 11 hrs.

Kindly have a look at my shared command and suggest the best way to run this tool faster on my data.

Thank you