taking longer and using more memory than expected

[jdmontenegro]

Dear all,

I am trying to use this tool for mapping RNAseq reads to a plant reference genome. I have 50 libraries with around 2.5Gb of data in each (2 x 100 bp). Most libraries were mapped quite easily using around 120GB of RAM and finished in 1-2 hours with 28 threads. However, a few libraries are problematic. They are either running out of time (>48h) or complaining of "Out of memory" even when they have over 256GB of RAM available.

Using other tools like STAR or tophat I didn't see any difference between running time or memory requirements in these libraries. Have you seen this behaviour before in any dataset? Is there any recommendation you could offer? Please see below details of the command line used. The reference genome was used to produce a Blast DB with "makeblastdb" and reads were aligned to the dataset.

makeblastdb -in ${assembly} -out ${ref} -dbtype nucl magicblast -query ${r1} -query_mate ${r2} -db ${ref} -infmt fastq -num_threads 28 -out ${out}

Kind regards,

Juan D. Montenegro