--numRequiredObs Exception #981
Description
Hello,
A labmate is trying to run salmon quant in a modified version of a script I wrote about a year ago and was able to run at the time w/o issue. He is now running into the following exception:
(mapping-based mode) Exception : [the argument ('from') for option '--numRequiredObs' is invalid].
We do not supply an argument for --numRequiredObs or --numRequiredFragments when submitting the job, and it is my understanding from scrolling through the source code that these options are now deprecated, but even when we explicitly set --numRequiredFragments to 50000000, we run into the same exception. Any tips to avoid this issue or idea of where it may be originating? We are working on an HPC cluster and running the following command:
salmon quant -i /projects/p31617/mm10/gencode.vM10.salmon.index -l A \ -1 ${samplename}_R1_001.fastq.gz \ -2 ${samplename}_R2_001.fastq.gz \ -o salmon_output/${samplename}_salmon \ -p 24 \ # this should match -n from SBATCH --seqBias \ --useVBOpt \ --validateMappings
Thank you!