RNA-Bloom v1.3.1
args: [-t, 12, -ntcard, -outdir, /my/output/dir, -long, /my/input/dir/nanosim_mouse_rna.fa.gz]

name:   rnabloom
outdir: /my/output/dir
WARNING: Output directory does not exist!
Created output directory at `/my/output/dir`

K-mer counting with ntCard...
Running command: `ntcard -t 12 -k 17 -c 65535 -p /my/output/dir/rnabloom @/my/output/dir/rnabloom.ntcard.readslist.txt`...
Parsing histogram file `/my/output/dir/rnabloom_k17.hist`...
Unique k-mers (k=17): 337,491,027
Min k-mer coverage threshold: 3
K-mer counting completed in 17.398s

Bloom filters          Memory (GB)
====================================
de Bruijn graph:       0.7458036
k-mer counting:        0.7842373
====================================
Total:                 1.530041

> Stage 1: Construct graph from reads (k=17)
[1] Parsing `/my/input/dir/nanosim_mouse_rna.fa.gz`...
[1] Parsed 442,245 sequences.
Parsed 442,245 reads in total.
DBG Bloom filter FPR:                 0.99947804 %
Counting Bloom filter FPR:            1.045231 %
> Stage 1 completed in 3m 13s

> Stage 2: Correct long reads for "rnabloom"
Parsing `/my/input/dir/nanosim_mouse_rna.fa.gz`...
Corrected Read Lengths Sampling Distribution (n=1000)
	min	q1	med	q3	max
	207	764	1127	1499	15641
Parsed 442,245 sequences.
	Kept:      409,197(92.52722%)
	Discarded: 33,048(7.4727807%)
	Artifacts: 83(0.018767878%)
> Stage 2 completed in 9m 11s

> Stage 3: Assemble long reads for "rnabloom"
Overlapped sequences: 373,549
         - discarded: 12,119
         - unique:    19,223
         - dovetail:  4,916
G: |V|=9,832 |E|=21,088
G: |V|=9,832 |E|=5,936
before: 408,972	after: 16,255
> Stage 3 completed in 25m 53s
Total runtime: 38m 35s