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Hello,
I am trying to perform a k-mer analysis using pysser for 6,240 bacterial genomes with binary phenotype. I'm having trouble running fsm-lite. The kmer count is using a lot of RAM and the process does not finish.
I use a Slurm-based cluster to submit jobs, so I need to declare how much memory and cpu my process will use. On the last attempt, I used 500 GB of RAM and it wasn't enough. Any suggestions to overcome this problem? Would increasing the number of cpus help?
The text was updated successfully, but these errors were encountered:
Yes, I managed to run the analysis using unitig-caller, but the result of mapping the unitgs to the reference genome using phandango_mapper was strange. Only 80 unitgs were mapped. In another analysis using a smaller data set, kmer's results were very positive, so I was trying to use the same strategy for this larger set.
Hello,
I am trying to perform a k-mer analysis using pysser for 6,240 bacterial genomes with binary phenotype. I'm having trouble running fsm-lite. The kmer count is using a lot of RAM and the process does not finish.
I use a Slurm-based cluster to submit jobs, so I need to declare how much memory and cpu my process will use. On the last attempt, I used 500 GB of RAM and it wasn't enough. Any suggestions to overcome this problem? Would increasing the number of cpus help?
The text was updated successfully, but these errors were encountered: