centrifuge-kreport issue finding parent of taxID

[mezewudo]

When I run the centrifuge-kreport to generate a kraken style from the output of the centrifuge analysis, I keep getting the sort of error message below. I will appreciate any guidance on what could be the issue:

Couldn't find parent of taxID 1048245 - directly assigned to root.
Couldn't find parent of taxID 1773 - directly assigned to root.

Thanks.

[mourisl]

What was your running command?

[mezewudo]

centrifuge-1.0.4.2/centrifuge-kreport -x centrifuge-1.0.4.2/hpvc ../output/test_sample.out > ../output/test_sample_report.txt

[mourisl]

Could you please run "centrifuge-inspect --taxonomy-tree centrifuge-1.0.4.2/hpvc | grep -w 1773" to check whether the taxonomy ID 1773 is in the taxonomy tree and has parent?

[mezewudo]

Here is the output when I run that command

765 | 1773 | no rank
1773 | 77643 | species
33894 | 1773 | no rank
83331 | 1773 | no rank
83332 | 1773 | no rank
336982 | 1773 | no rank
395095 | 1773 | no rank
419947 | 1773 | no rank
443149 | 1773 | no rank
443150 | 1773 | no rank
478433 | 1773 | no rank
478434 | 1773 | no rank
478435 | 1773 | no rank
652616 | 1773 | no rank
659019 | 1773 | no rank
707235 | 1773 | no rank
1010834 | 1773 | no rank
1010835 | 1773 | no rank
1010836 | 1773 | no rank
1138877 | 1773 | no rank
1249615 | 1773 | no rank
1306414 | 1773 | no rank
1427516 | 1773 | no rank
1445606 | 1773 | no rank

[mourisl]

This is very strange. The 1773 has the parent node 77643. Can you show me the first a few line of running log of centrifuge-inspect?

[mezewudo]

sorry, where can I find the log file for this?

[mourisl]

It's the print on the screen, like "loading taxonomy tree..."

[vanessariegel]

I also ran into the issue of "Couldn't find parent of taxID 79 - directly assigned to root.", but when using the centrifuge-inspect command it shows the correct parentID. Do you know what the issue here could be?

[mourisl]

Could you please show me the line from the centrifuge-inspect for the taxID 79?

[vanessariegel]

I'm using a custom database created for kraken2, so this is the line:
79 | 69 | family

It seems that everything is correct, but I still get that message.