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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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centrifuge-inspect warnings #161

Open BurinkiWU opened 5 years ago

BurinkiWU commented 5 years ago

Loading taxonomy ... Loading names file ... Loading nodes file ... Couldn't find parent of taxID 1826778 - directly assigned to root. Couldn't find parent of taxID 1606016 - directly assigned to root. Couldn't find parent of taxID 1649555 - directly assigned to root. Couldn't find parent of taxID 1649555 - directly assigned to root. Couldn't find parent of taxID 319938 - directly assigned to root. What is the problem with it?

My command was attached below: $ centrifuge-kreport -x /home/disk3-8T/wzq/centrifuge_1.0.3/nt < RMD_0-10_nt.report.txt > RMD_0-10_centrifuge_nt_test.txt_kreport Reading centrifuge out file from STDIN ... Loading taxonomy ... Loading names file ... /usr/local/bin/centrifuge-inspect:24: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp

mourisl commented 5 years ago

There are some taxonomy ids got deprecated from the taxonomy tree but they might still put it there, e.g.: https://www.ncbi.nlm.nih.gov/taxonomy/?term=1826778. So it is normal to see this warning.

BurinkiWU commented 5 years ago

But the output file *.txt_kreport can not be used for the pavian drawing profile, what makes this problem?

mourisl commented 5 years ago

Can you show me the few lines of RMD_0-10_nt.report.txt and RMD_0-10_centrifuge_nt_test.txt_kreport?

BurinkiWU commented 5 years ago

Thanks, I have just fixed my problem.

chaichai9521 commented 4 years ago

Hi BurinkiWU,

how did you fix the problem "Couldn't find parent of taxID 1826778 - directly assigned to root."? I met same problem when run 'centrifuge-kreport'

Kumereng commented 3 years ago

Hi. I get this: "Couldn't find parent of taxID 46170 - directly assigned to root." Please help as I get a low classification for the actual species.