error in the file *.combine.scn

[ericgonzalezs]

Hello,

I am running LTR_FINDER_parallel like this:

LTR_FINDER_parallel -seq ARG.fa -threads 10 -harvest_out -size 1000000 -time 300

However the file ARG.fa.finder.combine.scn only contains the header.

#LTR_FINDER_parallel -seq ARG.fa -size 1000000 -time 300 -try1 1 -harvest_out -threads 10 -cut /project/6019339/egonza02/bin/software/LTR_retrieve r/LTR_FINDER_parallel/LTR_FINDER_parallel/bin/cut.pl -finder /project/6019339/egonza02/bin/software/LTR_retriever/LTR_FINDER_parallel/LTR_FINDER_p arallel/bin/LTR_FINDER.x86_64-1.0.7/

LTR_FINDER args=-w 2 -C -D 15000 -d 1000 -L 7000 -l 100 -p 20 -M 0.85

LTR_FINDER_parallel version=v1.2

predictions are reported in the following way

s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr chr

where:

s = starting position

e = ending position

l = length

ret = LTR-retrotransposon

lLTR = left LTR

rLTR = right LTR

sim = similarity

seq-nr = sequence order

I read in another issue that the problem could be the file name. However, I am not sure how short the file name should be. My file name is already very short. Any help with this would be great.

Best Wishes,

Eric

[oushujun]

Hi Eric,

Please give some examples of your sequence names in the genome. Thank you.

Shujun

[mattheatley]

just to add to this - I had a similar issue that was solved by using simple sequence ids (e.g. seqkit seq --only-id)