How to stop error correction

[sanyalab]

Hello,

I am already using Pacbio FLNC reads that are quite accurate. I therefore do not need error correction with Illumina short reads. Is there any way to turn off the error correction of Stage 2? I tried using -e 0 but it seems it is still taking it up for correction. Please advice. Here is a snippet of what I am observing

Parsing `/data/DATASETS/TESTING/Sample1_modi2.fa`...
Parsed 10,064,939 sequences in 17m 14s
Parsed 123,796,711 sequences from 3 files.
DBG Bloom filter FPR:                 0.777 %
Counting Bloom filter FPR:            0.762 %
Saving graph to disk `/data/DATASETS/TESTING/RNAB_OUT_E0/Sample1.graph`...
> Stage 1 completed in 33m 30s

> Stage 2: Correct long reads for "Sample1"
Parsing `/data/DATASETS/TESTING/Sample1_modi2.fa`...
Corrected Read Lengths Sampling Distribution (n=10000)
	min	q1	med	q3	max
	179	781	1189	1472	9807
Parsed 10,064,939 sequences.
	Kept:      10,064,903	(100.0 %)
	Discarded: 36	(3.58E-4 %)
	Artifacts: 217	(0.0021559992%)
Corrected reads in 7m 13s
Extracting seed sequences...
strobemers: n=3, k=11, wMin=12, wMax=61, depth=10

My command below

DIR=$(pwd); bsub -R "rusage[mem=8000]" -R "span[hosts=1]" -n 16 -J "RNAB_PASS1" -o $DIR/rnabloom_e0.out%J -e $DIR/rnabloom_e0.err%J "export JAVA_TOOL_OPTIONS='-Xmx100g'; /home/miniforge3/envs/mRNAClustEnv/bin/rnabloom -long /data/DATASETS/TESTING/Sample1_modi2.fa -l /data/DATASETS/TESTING/Sample1-pairsR1.fq.gz -r /data/DATASETS/TESTING/Sample1-pairsR2.fq.gz -savebf -ss -lrpb -a 0 -e 0 -lrrd 3 -lrsub 10,s,11,50 -p 0.98 -fpr 0.005 -length 180 -t 24 -n Test -prefix Test1 -o `pwd`/RNAB_OUT_E0"

Thanks
Abhijit

[kmnip]

Since you used -e 0, the error correction step actually performed no real error corrections. RNA-Bloom still has to go through your reads as part of stage 2.