We faced this problem with the many contigs of Striacosta, and ultimately aborted that species, but we should try to fix this anyway at some point.
templates/merge_consensus.sh was generating a huge .command.run file when ${windows_fasta} expanded to each individual contig.
cat ${windows_fasta} > ${outdir}_consensus.fasta
If .command.run is larger than a certain default value > 5MB, the cluster scheduler produces an error:
sbatch: error: Batch job submission failed: Pathname of a file, directory or other parameter too long
We faced this problem with the many contigs of Striacosta, and ultimately aborted that species, but we should try to fix this anyway at some point.
templates/merge_consensus.shwas generating a huge.command.runfile when${windows_fasta}expanded to each individual contig.cat ${windows_fasta} > ${outdir}_consensus.fastaIf
.command.runis larger than a certain default value > 5MB, the cluster scheduler produces an error:sbatch: error: Batch job submission failed: Pathname of a file, directory or other parameter too longAnother example of the same issue in a different pipeline More generally discussed here