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Describe the bug
I am trying to rum zUMI's on a large cluster with SLURM. They do not allow anaconda so i cannot use the in-build conda env.
Instead we can install required software in our $HOME folder and load software modules available on the server.
I am running on a small dataset i have used before and am now using as test-data because it is a small dataset (SRR6750041).
When running STAR seems to get a segmentation fault during the mapping stage, and i am not sure why?
Did you see this behaviour before? I cannot find anything similar in on STAR github
I can only find a Log.final.out in zUMI's output which is an empty file. There does not seem to be another STAR Logfile.
One other strange behaviour is that the genome is generated with the same STAR that is loaded, so i am not sure why the STARgenome version is not the same warning pops up.
Describe the bug
I am trying to rum zUMI's on a large cluster with SLURM. They do not allow anaconda so i cannot use the in-build conda env.
Instead we can install required software in our $HOME folder and load software modules available on the server.
I am running on a small dataset i have used before and am now using as test-data because it is a small dataset (SRR6750041).
When running STAR seems to get a segmentation fault during the mapping stage, and i am not sure why?
Did you see this behaviour before? I cannot find anything similar in on STAR github
I can only find a Log.final.out in zUMI's output which is an empty file. There does not seem to be another STAR Logfile.
One other strange behaviour is that the genome is generated with the same STAR that is loaded, so i am not sure why the STARgenome version is not the same warning pops up.
Kind regards,
Lucas
To Reproduce
The sbatch.sh
the YAML
Screenshots
The stdout and error is readable here
slurm-2742904.txt
Desktop (please complete the following information):
Additional context
Add any other context about the problem here.
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