GERP++ (gerpcol) error on a test data
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6.3 years ago
kirill1984 ▴ 10

Hi guys,

I'm wondering if there's a tutorial or experienced users of GERP++ as I'm doing something wrong and need your help.

In particular, I can't get GERP++ work even on a test data set

For example, when I run first part of the pipeline as gerpcol -f ENr111.aln -t ENr111.tree -e rfbat -j human
I get following:
Tree species armadillo not present in alignment and therefore ignored. Tree species baboon not present in alignment and therefore ignored. Tree species cat not present in alignment and therefore ignored. Tree species chimp not present in alignment and therefore ignored. Tree species colobus_monkey not present in alignment and therefore ignored. Tree species cow not present in alignment and therefore ignored. Tree species dog not present in alignment and therefore ignored. Tree species dusky_titi not present in alignment and therefore ignored. Tree species elephant not present in alignment and therefore ignored. Tree species galago not present in alignment and therefore ignored. Tree species guinea_pig not present in alignment and therefore ignored. Tree species hedgehog not present in alignment and therefore ignored. Tree species human not present in alignment and therefore ignored. Tree species macaque not present in alignment and therefore ignored. Tree species marmoset not present in alignment and therefore ignored. Tree species monodelphis not present in alignment and therefore ignored. Tree species mouse not present in alignment and therefore ignored. Tree species mouse_lemur not present in alignment and therefore ignored. Tree species owl_monkey not present in alignment and therefore ignored. Tree species rabbit not present in alignment and therefore ignored. Tree species rat not present in alignment and therefore ignored. Tree species rfbat not present in alignment and therefore ignored. Tree species sbbat not present in alignment and therefore ignored. Tree species shrew not present in alignment and therefore ignored. Tree species st_squirrel not present in alignment and therefore ignored. Tree species tenrec not present in alignment and therefore ignored. Processed alignment of 0 positions.

It's odd as the alignment has those seqs:
grep ">" ENr111.aln :

human
chimp
colobus_monkey
baboon
macaque
dusky_titi
owl_monkey
marmoset
mouse_lemur
galago
rat
mouse
guinea_pig
st_squirrel
rabbit
cow
cat
dog
sbbat
rfbat
hedgehog
shrew
armadillo
tenrec
elephant
monodelphis

Do you have any ideas what is wrong and how to fix it?

Thanks.

GERP++ GERP GERP+ • 3.4k views
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1
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6.2 years ago
robert.young ▴ 10

I just found your question while googling the same error message. In case you're still struggling, I discovered that you need to add the '-a' flag to get gerpcol to read .fa files.

So, if you modify your command to :

gerpcol -a -f ENr111.aln -t ENr111.tree -e rfbat -j

it should run. It did for me at least!

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0
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your message solved it, but now I'm getting this error:

Segmentation fault (core dumped)
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or could you tell me what's your reference sequence? Could be that I'm not adding the correct one

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10 months ago
gubrins ▴ 260

Heys, I know is a bit out of the topic but what's the structure of the alignment files? I am not able to download the test data and my alignment file is not being accepted by the program. Thanks!

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