cdhit

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Problems during running PSI-CD-HIT:Name "main::bl_dir" used only once: possible typo at ./psi-cd-hit.pl line 103.

5

After entering the command according to the user's guide,psi-cd-hit produce output files,but there is no clustering. ### ./psi-cd-hit.pl -i /root/yzm/dataset/db_60.fasta -o /root/yzm/dataset/db_25 -c 0.25 -ce 1e-5 -g 1 > Output:...

AL-Yan

How to reset MAX_SEQ

3

https://github.com/weizhongli/cdhit/issues/97 Here it states to remove the .o file before make MAX_SEQ=10000000, but i can`t find where .o file is. Hope for your guidance, thanks！

timeresistance1996

error after making max-seq 1000000

1

Hi, I ran "git clone https://github.com/weizhongli/cdhit.git" Then, changed the directory to cdhit. Then ran "make MAX_SEQ=10000000" I got ``` "g++ -fopenmp -DWITH_ZLIB -O2 -DMAX_SEQ=10000000 cdhit-common.c++ -c g++ -fopenmp -DWITH_ZLIB -O2...

Ahmedbargheet

cd-hit-est does not produce output files

9

cd-hit-est does not produce an output file, only the Usage pops up after entering the command: cd-hit-est [Options] (base) dell@dell-R730:~/metagenome$ cd-hit-est -i prodigal/final.contigs.genes -o NR/NR.ncu.fa -c 0.95 -aS 0.9 -d...

songzhang-master

FATAL docker build error

1

Hello, I am trying to install cd-hit on my University's computing cluster using this command: `singularity exec docker build --tag cd-hit https://raw.githubusercontent.com/weizhongli/cdhit/master/Docker/Dockerfile ` But I receive this error. FATAL: could...

steph-birnbaum

Greetings! I have installed CD-HIT with ```conda install -c bioconda cd-hit``` and can't find the ```psi-cd-hit.pl``` executable. Running ```find ~/anaconda3/envs/hmm -name "psi*"``` finds no such file, has this been removed...

iquasere

Running cd-hit with 26Gb data set is too slow

5

My nucleic acid data set is about 26Gb with 29,938,643 sequences. The software has been running for a month with the parameter of '-T 85 -M 100000 -c 0.9', but...

biolittleboy

CD-HIT-EST not allowing below 80% cutoff

2

I have been running the program applying various nt-identity cutoff values and the cd-hit-est does not allow for below 80%. Here is an exact example: cd-hit-est -i /home/path/VP3.fasta -o /home/path/VP3.fasta...

roelofco

Hello, I was wondering if it's possible to save the index table with the k-mers generated from input sequences to disk and later retrieve it, in order to speed up...

sysimm

Hi, I have installed cd-hit via Conda and when I try to run cd-hit-est I get the following error: *** Error in `cd-hit-est': corrupted double-linked list: 0x0000559009582520 *** I ran...

SebasSaenz