forcing read error correction using SPAdes

Question

[jen]

Given that this is my code below, why is SPAdes giving me the following message?:

Mode: ONLY assembling (without read error correction) Debug mode is turned OFF

I would like for the assembly to complete the read error correction step if possible. Based on what I have read online, the read correction step is the default, so I don't know what to change in my code or if there's anything I should specify to force the step. Could it be that rnaviralspades prohibits the read correction step? Any help is appreciated, thanks!

 nice -n12 /usr/local/bin/rnaviralspades.py --pe-1 1 /nas2/blue_crab_chunglab/mingli_data/RNA/FL_Dec_2021_1.fq.gz --pe-2 1 /nas2/blue_crab_chunglab/mingli_data/RNA/FL_Dec_2021_2.fq.gz --pe-1 2 /nas2/blue_crab_chunglab/mingli_data/jen_data/LARNA1104/LARNA1104_1.fq.gz --pe-2 2 /nas2/blue_crab_chunglab/mingli_data/jen_data/LARNA1104/LARNA1104_2.fq.gz --pe-1 3 /nas2/blue_crab_chunglab/mingli_data/jen_data/MDRNA1104/MDRNA1104_1.fq.gz --pe-2 3 /nas2/blue_crab_chunglab/mingli_data/jen_data/MDRNA1104/MDRNA1104_2.fq.gz -t 12 -o /data/users/jherrera/FL_LA_MD_10/RNA_spades

Answer 1

[Mensur Dlakic]

Could it be that rnaviralspades prohibits the read correction step?

That appears to be the case. If you run spades.py -h, among other switches it will print the following:

--rnaviral (same as rnaviralspades.py) This flag should be used when assembling viral RNA-Seq data 
sets (runs rnaviralSPAdes). Not compatible with --only-error-correction or --careful options.

If it can't do --only-error-correction, one could interpret that to mean it can't do error correction at all.

[jen]

I was thinking along the same lines, but was hoping that wasn't the case. Thanks a lot!