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Error when running cdd2cog #13

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ngilber3 opened this issue Dec 18, 2019 · 0 comments
Open

Error when running cdd2cog #13

ngilber3 opened this issue Dec 18, 2019 · 0 comments

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@ngilber3
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Hi, I am trying to run cdd2cog and I am getting the Error: Excessively long <> operator at ./cdd2cog.pl line 21

I am running: $ perl ./cdd2cog.pl -r GRW1_COGs_rpsblast.out -c cddid.tbl -f fun.txt -w whog -a

I got the rpsblast output by running: rpsblast -i ../proteins/GRW1_prots.fas -d Cog_LE/Cog -o GRW1_COGs_rpsblast.out -e 0.01 -m 8

I notice that the outfmt parameter written in the README file for running RPS-BLAST says to use "-outfmt 6 or 7", but when I tried running this option it did not want to take it.

Here are the first few lines of the GRW1_COGs_rpsblast.out:
gene_3|GeneMark.hmm|389_aa|+|1295|2464 >k123_143 gnl|CDD|226020 17.25 313 213 12 105 389 65 359 2e-05 42.9
gene_6|GeneMark.hmm|322_aa|-|993|1961 >k123_238 gnl|CDD|224392 21.43 140 92 3 70 209 16 137 5e-08 49.9
gene_7|GeneMark.hmm|235_aa|-|1975|2682 >k123_238 gnl|CDD|224113 21.79 179 126 2 20 198 76 240 2e-19 81.8

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