I would like to assemble RNA-seq data de novo using Trinity. I got paired-end reads (44 million). The problem is that I keep having this error message:
Error, cmd: /usr/local/bin/trinityrnaseq_r2011-07-13/Chrysalis/Chrysalis -i both.fa -iworm inchworm.K25.L48.DS.fa -o chrysalis -min 200 -dist 300 -butterfly /usr/local/bin/trinityrnaseq_r2011-07-13/Butterfly/Butterfly.jar died with ret 11 at Trinity.pl line 459.
Error 11 being "Try Again" in Linux.
This is the command I ran:
sudo perl Trinity.pl --seqType fa --left No_Hits_reads1.fasta --right No_Hits_reads2.fasta --CPU 6 --run_butterfly --bflyHeapSpace 10G
As suggested in the documentation I set the stacksize to unlimited (ulimit -s unlimited), as you can see below:
core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 20 file size (blocks, -f) unlimited pending signals (-i) 16382 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) unlimited virtual memory (kbytes, -v) unlimited file locks (-x) unlimited
Do you guys have any idea on how to solve this problem ? I have "only" 24 Gb of RAM, could that be a problem ?