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cd-hit-est -d description length option not working #134

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Vicbuz opened this issue Dec 1, 2022 · 1 comment
Open

cd-hit-est -d description length option not working #134

Vicbuz opened this issue Dec 1, 2022 · 1 comment

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@Vicbuz
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Vicbuz commented Dec 1, 2022

Hello, I am using cd-hit-v4.8.1-2019-0228. The command -d command does not appear to change the length of the description in the resulting cluster file in cd-hit-est.
my command is:

./cd-hit-est -i 16S_rRNA_all.fasta -o 16S_rRNA_all_c99.fasta -c 0.99 -M 16000 -d 250

I have also tried

/cd-hit-est -i 16S_rRNA_all.fasta -o 16S_rRNA_all_c99.fasta -d 200 -c 0.99 -M 16000

and:

'/cd-hit-est -i 16S_rRNA_all.fasta -o 16S_rRNA_all_c99.fasta -d 100 -c 0.99 -M 16000'
If I change the other commands, they work but it always produces the same default description length of 20 in the .clstr file. An example of which is below:

Cluster 0
0 3600nt, >NG_046384.1... *
Cluster 1
0 2211nt, >NG_041958.1... *
1 2207nt, >NG_041961.1... at +/99.00%
Cluster 2
0 2197nt, >NG_042068.1... *
Cluster 3
0 2192nt, >NG_042067.1... *
1 2130nt, >NG_041954.1... at +/99.95%
Cluster 4
0 2192nt, >NG_041957.1... *
1 2168nt, >NG_041951.1... at +/99.68%
Cluster 5
0 2089nt, >NG_044969.1... *
Cluster 6
0 1833nt, >NG_042881.1... *
1 1676nt, >NG_042880.1... at +/99.94%
Cluster 7
0 1774nt, >NR_121591.1... *
1 1768nt, >NR_044618.1... at +/99.10%
Cluster 8
0 1769nt, >NR_117659.1... *
Cluster 9
0 1760nt, >NG_042882.1... *

@kostrouc
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kostrouc commented Dec 9, 2022

I am also obtaining the same output when running cd-hit with the -d parameter not set to the default value.

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