Comments (6)
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.
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Thanks for answering!!!!! π₯° and for your timeπ
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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!
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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.
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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
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Related Issues (20)
- centrifuge download fails HOT 2
- The second file of customer db is empty HOT 4
- Database download taking a lot of disk space + taking too long HOT 3
- not able to build database, taxonomy does not exist warnings, latest version by git HOT 1
- M. tuberculosis genome size error
- Unrecognised `--temp-directory` option, however specified in code? HOT 9
- ERROR): Expected centrifuge to be in same directory with centrifuge-class: HOT 2
- Database problem HOT 1
- Database question HOT 10
- Can using "--mm" flag reduce memory usage? HOT 2
- NCBI nt index HOT 6
- option --packed
- nt index incomplete build HOT 21
- centrifuge-kreport values do not ad HOT 3
- how do i setup the SILVA database? HOT 4
- Centrifuge Classifying Reads, but the Report is Empty HOT 3
- Viral new File format? HOT 4
- centrifuge-inspect python script is incompatible with python >=3.12 HOT 2
- Issues with Centrifuge Output for Functional Annotation HOT 2
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