cdhit

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Problem compiling on MacOS 10.14.6

2

I am unable to compile cd-hit-v4.8.1-2019-0228, regardless of GCC version (I have tried with GCC 9, 8, and 6, all installed by Homebrew). Any help is appreciated. Thanks, Sam ```bash...

semiller10

I am trying to cluster the NR database with following parameters on the Bridges supercomputer but got the error: `Detected 1 oom-kill event(s) in step 9869759.batch cgroup. Some of your...

hamid58b

First Iteration doesn't processed in multi-threading mode.

2

I'm running CD-HIT on a 17GB RNA sequences multifasta file on a Core i9 Processor with 32 Cores. I'm wondering why CD-HIT does not use the whole cores in the...

mr-eyes

Install problem in MacOs

1

I already install gcc and use commend : make CC=/usr/local/Cellar/gcc/9.3.0_1/bin/gcc-9 to compile. But it failed. The error information is : ld: symbol(s) not found for architecture x86_64 collect2: error: ld...

WiseHolo

CD-HIT not working (empty error file)

1

I have a very large multi-FASTA file containing many replicate nucleotide sequences. With smaller files, I've dealt with duplicates using BBedit, but this file is way too big to do...

sjfleck

I was running code like below to remove sequences that is a part of a longer ones. ``` cd-hit -i seq -o seqout -c 1.0 -n 5 -M 25000 -T...

ATPs

total_seq report is erroneous

1

When initiating CD-HIT-EST over a large FASTA file, the total seq report is mistaken. I have a large dataset that I have partitioned into multiple files using [SeqKit split2](https://bioinf.shenwei.me/seqkit/usage/#split2). Every...

jmonroynieto

cd-hit-est Segmentation fault

1

cd-hit version:4.8.1 command: cd-hit-est -i Megahit/STA-004A/final.contigs.fa -o CD_Hit/STA-004A_c95 -c 0.95 -n 10 -d 0 -T 8 &>CD_Hit/STA-004A.log & The input contigs file size 404M,it raisen the "Segmentation fault" ,how can...

neptuneyt

I'm trying to cluster ~1 million protein sequences with identity of 50%. When I've clustered by 60% identity I've used n=4 and it took few hours with 20 threads. But...

YiJessePi

Hello, I installed both gcc 5 and 6 with `brew` and tried to compile with: `make CC=/usr/local/Cellar/gcc\@6/6.5.0_2/bin/g++-6` or `make CC=/usr/local/Cellar/gcc\@5/5.5.0_3/bin/g++-5`, and get the same error message for both: ``` /usr/local/Cellar/gcc@5/5.5.0_3/bin/g++-5...

edgardomortiz