User: guardsquirrel

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Posts by guardsquirrel

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Comment: C: Time ran out in SLURM operation
... Thank you so much for all your help, I really appreciate it! :) ...
written 11 weeks ago by guardsquirrel0
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Comment: C: Time ran out in SLURM operation
... OHHH! I'm so sorry I didn't see the parallelising section in the manual, so in my run script I have: srun --export=ALL orthofinder -f species/ but it should actually be `srun --export=ALL orthofinder -f species/ -t 28`? ...
written 11 weeks ago by guardsquirrel0
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Comment: C: Time ran out in SLURM operation
... From a SLURM shell script. It doesn't have the -t and -a parameters but it has #SBATCH --ntasks=1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=28 #SBATCH --time=24:00:00 (I've tried extending this but the maximum allocation time is 24 hours) I'm not really sure what to c ...
written 11 weeks ago by guardsquirrel0
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Comment: C: Time ran out in SLURM operation
... Thank you so much for your answer, my cluster does unfortunately have a max time allocation of 24 hours.. Basically I'm running OrthoFinder on the protein fasta files of 5 species... I was wondering if changing the ntasks/ntasks per node/cpus per task parameters would make me able to complete the j ...
written 11 weeks ago by guardsquirrel0
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Time ran out in SLURM operation
... Hello! I'm extremely new to SLURM and bioinformatics so apologies for this rather dumb question and if I use any terminology wrong (feel free to correct me)! Basically I ran a SLURM operation, however it surpassed the allocated 24 hours on the HPC server I'm using and ran out of time... Here are s ...
software error multithreading parallel slurm written 11 weeks ago by guardsquirrel0
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How to find which genes are missing?
... Hi everyone, I've made an assembly for a chloroplast genome, however I'm confused as to what I have to do next... I'm trying to identify any genes that are normally present in chloroplasts but are missing in my assembly. How could I go about doing this? Thank you so much. ...
genome assembly alignment gene chloroplast written 10 months ago by guardsquirrel0 • updated 11 weeks ago by Mensur Dlakic5.8k

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