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?