[Inchworm-users] inchworm runtimes

[Dana P. <dan...@gm...>]

I've got 42 million Illumina paired end reads (84 million total) of
125x125bp, and ran the trinity pipeline via

/usr/local/bin/Trinity.pl --seqType fq --left left.fastq --right
right.fastq  --output output --run_butterfly --num_butterfly_CPU 48
--min_contig_length 100

It's running inchworm, via

/usr/local/bin/Inchworm/bin/inchworm --reads both.fa --run_inchworm -K 25 -L
48 --monitor 1  --DS  2>monitor.out > inchworm.K25.L48.DS.fa

That's been running for 3 days on a 48 cpu AMD Opteron 2.1GHz SMP machine.
It spawned 48 threads for the first two days.  Today I see that the number
of threads has dropped to 1.  It's got a 74 gig memory footprint.  I'm
wondering if it's still doing anything?  Is a three day assembly
par-for-the-course with this much data?

Thanks!


-- 
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu