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Updated dbcan dependencies resulted in less cazy being detected with the hotpep tool.
I just updated the dependencies for dbcan today to what is on the readme document and re ran on the same set of genomes and everything worked fine. But upon inspection of the hotpep outputs there is now only 82 vs 201 prior to the update. What would have resulted in such a big difference?
Could you show me the previous database and dependencies you used? Thanks a lot. And if you can provide your command it will be fine.
This is an old issue so I don't know what the original version was, but today I upgraded from 2.0.6 to 2.0.11 and it did not decrease hotpep detection in my organism
tail -n +2 dbcan_results_2.0.11/cazyHotpep.out | cut -f 1 | sort | cut -c-2 | uniq -c
12 AA
89 CB
18 CE
146 GH
51 GT
14 PL
tail -n +2 dbcan_results_2.0.6/cazyHotpep.out | cut -f 1 | sort | cut -c-2 | uniq -c
15 AA
18 CE
137 GH
14 PL
Only superfamilies I "lost" results were for AA, and this was not straightforward because the classifications are a bit different
egrep "^AA" dbcan_results_2.0.11/cazyHotpep.out | cut -f 1,2 | sort | uniq -c | sed "1 i count\tCAZy_fam\tPPR_subfam" -
count CAZy_fam PPR_subfam
1 AA1 4
1 AA3 2
2 AA3 8
2 AA6 1
5 AA6 2
1 AA6 4
dbcan_results_2.0.6/cazyHotpep.out
count CAZy_fam PPR_subfam
1 AA1 2
3 AA3 1
1 AA3 3
2 AA6 3
4 AA6 5
4 AA8 3
And they're a bit different for other superfamilies too, really just at the subfamily level though...
egrep "^CE" dbcan_results_2.0.11/cazyHotpep.out | cut -f 1,2 | sort | uniq -c | sed "1 i count\tCAZy_fam\tPPR_subfam" -
count CAZy_fam PPR_subfam
2 CE11 12
1 CE4 1
4 CE5 17
11 CE8 30
dbcan_results_2.0.6/cazyHotpep.out
count CAZy_fam PPR_subfam
1 CE11 14
1 CE4 1
1 CE4 95
4 CE5 9
11 CE8 22