Couldn't find parent of taxID 138 - directly assigned to root. about centrifuge HOT 6 CLOSED

Thank you for catching this error! I think I made a mistake in assuming that field is for parent taxonomy ID in parsing SILVA tree structure. I will update the script today or tomorrow, and you can recreate the index and give it a try. Sorry for the trouble.

from centrifuge.

Thanks for answering!!!!! 🥰 and for your time😀

from centrifuge.

I have updated the script at: https://github.com/mourisl/centrifuger/tree/master/indices/silve-download.pl. Could you please give it a try? Thank you!

from centrifuge.

Hi!, i just run it:

it gave me this error:

[mdavid@mapudungun-frontend centrifuge]$ perl silva-download.pl
Bareword found where operator expected at silva-download.pl line 11, near "data"
(Missing semicolon on previous line?)
Bareword found where operator expected at silva-download.pl line 11, near ""auto" data"
(Missing operator before data?)
Bareword found where operator expected at silva-download.pl line 11, near ""light" data"
(Missing operator before data?)
Bareword found where operator expected at silva-download.pl line 12, near "data"
(Missing semicolon on previous line?)
Bareword found where operator expected at silva-download.pl line 12, near ""system" data"
(Missing operator before data?)
Bareword found where operator expected at silva-download.pl line 39, near "" src="https"
(Missing operator before https?)
Bareword found where operator expected at silva-download.pl line 39, near "74354d43143c"
(Missing operator before d43143c?)
String found where operator expected at silva-download.pl line 39, near "<script crossorigin=""
(Missing semicolon on previous line?)
Bareword found where operator expected at silva-download.pl line 40, near "<script crossorigin="anonymous"
(Might be a runaway multi-line "" string starting on line 39)
(Missing operator before anonymous?)
String found where operator expected at silva-download.pl line 40, near "anonymous" defer=""
Bareword found where operator expected at silva-download.pl line 40, near "" defer="defer"
(Missing operator before defer?)
String found where operator expected at silva-download.pl line 40, near "defer" type=""
Bareword found where operator expected at silva-download.pl line 40, near "" type="application"
(Missing operator before application?)
String found where operator expected at silva-download.pl line 40, near "javascript" src=""
Bareword found where operator expected at silva-download.pl line 40, near "" src="https"
(Missing operator before https?)
Can't modify numeric lt (<) in scalar assignment at silva-download.pl line 11, near "data"
syntax error at silva-download.pl line 11, near "data"
Unknown regexp modifier "/j" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/v" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/r" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/t" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/t" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/h" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/b" at silva-download.pl line 39, at end of line
Unknown regexp modifier "/t" at silva-download.pl line 40, at end of line
silva-download.pl has too many errors.

from centrifuge.

It seems what you downloaded from the github is not the script itself but the link information. I guess you used "wget" on the link. You can use "git pull" to update the script if you previously used git clone.

from centrifuge.

thanks, now it works! thanks thanks thanks

from centrifuge.