Sam Nooij

tldr; The gbk2faa.pl script uses a locally installed perl (/usr/bin/perl), which did not work on the machine I use. I modified the command to use the conda-installed perl. --- When...

Save disk space by compressing fastq files (after trimming and filtering)

5

With large datasets and limited disk capacity, saving intermediate fastq files as raw fastq may take up hundreds of GBs of disk space. Disk usage may be decreaused by using...

'grid' mode does not seem to work with Open Grid Scheduler

5

I have been trying to get Jovian up and running on a cluster with Open Grid Scheduler, and now DRMAA is giving me this error when trying to submit the...

Fresh install does not work: DistributionNotFound (xgboost)

2

I just installed CCTyper through conda/mamba and unfortunately it won't run at all. To be precise, I ran the command `mamba env create -f cctyper.yaml` and the contents of `cctyper.yaml`...

Jaeger uses more threads than assigned (with GNU parallel)

5

I'm running Jaeger on bacterial genomes using GNU parallel with 1 CPU assigned to each Jaeger process. However, `top` indicates that each process may consume more than 30 threads for...