I'm currently using Rsubread (and the standalone programs) to process some RNA-Seq data. Everything seems OK, but some doubts emerged.
After running the subjunc aligner with this command:
subjunc -i ../../genomes/UCSC/hg19/Rsubread/hg19.Rsubread.idx -r Thiago_ACTTGA_L008.fastq.gz --gzFASTQinput --BAMoutput --allJunctions -H -Q -u -I 17 -T 16 -o Thiago.subjunc
I've got this error at the very end of the running:
subjunc: core-indel.c:1568: write_indel_final_results: Assertion `rlen<900' failed.
But, the results seem all fine when compared with a previous run with default indel parameter. I've looked at the source code and wasn't able to understand what happened. Could someone give me a light about this issue?
Another interesting point is the hard limit on the number of threads. My machine has 64 cores and I could only use 32 on a given run of subread-align/subjunc. At first, I've thought it was some issue with my R installation. This behavior persists in the standalone programs. Is there some flag/parameter where I can reset the hard limit?
Thanks for the explanations. I'll adjust my parameters. We're interested in small indels at this moment. But, all my samples (cases and controls) seem to possess long indels. About threads, after some testing, I've sticked to 16 threads per sample, with four samples per node running at the same time. Looks good enough for me.