Error while primer removal about lrasmanuscript HOT 7 CLOSED

Does this error get triggered by every file? i.e. what happens if you remove the loop and just try fns[[1]] and nops[[1]].

What is the output of head(fns) and head(nops)?

from lrasmanuscript.

So with the loop the output would be

head(fns)
[1] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.0_0.fastq.gz"
[2] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.1_1.fastq.gz"
[3] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.10_10.fastq.gz"
[4] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.11_11.fastq.gz"
[5] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.12_12.fastq.gz"
[6] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.13_13.fastq.gz"

head(nops)
[1] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.0_0.fastq.gz"
[2] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.1_1.fastq.gz"
[3] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.10_10.fastq.gz"
[4] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.11_11.fastq.gz"
[5] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.12_12.fastq.gz"
[6] "/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.13_13.fastq.gz"

and instead of using the loop i now tried the following:

fn <- fns[[3]]; nop <- nops[[3]]
dada2:::removePrimers(fn, nop, primer.fwd=FWD, primer.rev=dada2:::rc(REV), orient=TRUE)
Error in sapply(match.fwd, end) + 1 :
non-numeric argument to binary operator

whereas:

head(nop)
[1] "~/OneDrive - Syddansk Universitet/HzsA/packed//noprimers/demux_ccs.10_10.fastq.gz"
head(fn)
[1] "/Users/schauberger/OneDrive - Syddansk Universitet/HzsA/packed//demux_ccs.10_10.fastq.gz"

from lrasmanuscript.

And yes unfortunately it gets triggered by every file

from lrasmanuscript.

Not sure. Can you share one file with me (one of the fns) so that I can reproduce it on my end?

from lrasmanuscript.

Hi,

I hope i have used the correct email :)
and thank you so much helping with this 👍

from lrasmanuscript.

The immediate issue is that your FWD and REV primer sequenced you've provided are not in your sequencing data. Are you sure these primers were used? Were primers perhaps already removed by another software tool?

Edit: Added a check for this condition (no primer matches) to the function in benjjneb/dada2@9c22747

from lrasmanuscript.

from lrasmanuscript.