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Can't convert CDDs IDs to COGs #10

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iquasere opened this issue Oct 1, 2018 · 0 comments
Closed

Can't convert CDDs IDs to COGs #10

iquasere opened this issue Oct 1, 2018 · 0 comments

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@iquasere
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iquasere commented Oct 1, 2018

Following all the commands in #1 , I get rpsblast claiming that the arguments in the command "rpsblast -query GCF_000005845.2_ASM584v2_protein.faa -db Cog -out rps-blast.out -evalue 1e-2 -outfmt 6" are wrong, and it works after I adjust the command to

rpsblast -i GCF_000005845.2_ASM584v2_protein.faa -d Cog -o rps-blast.out -m 8

which gets the job done, however the conversion to COGs with

perl cdd2cog.pl -r rps-blast.out -c cddid.tbl -f fun.txt -w whog

gets the result

Overall assignment statistics:
~ Total query proteins categorized into COGs: 4134
~ Total COGs used for the query proteins [of 4873 overall]: 1
~ Total number of assigned functional categories: 0
~ Total functional categories used for the query proteins [of 25 overall]: 0

which brings no information, since nothing was identified. It also outputs a lot of "Use of uninitialized value" which probably means the CDD's IDs are not being recognized. The rest of the commands were used as suggested, so what is happening here? Also, this is using the 2003 COGs right?

@iquasere iquasere closed this as completed Oct 1, 2018
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