Why cd-hit-est not work when sequence identity threshold<0.95？

Question

[JZX]

The fasta file is about 500M， The longest is about 100000, Memory=60G CPU=16 cores

It runs normal when -c = 0.95 or 0.99 But it became very slow when -c =0.9, and the CPU and the speed of the hard disk show it didn't work.

cd-hit-est -M 60000 -T 16 -c 0.9 -n 8 -g 0 -i input -o output

Answer 1

[weidonglu]

The time for cd-hit-est analysis with -c =0.9 is much longer those with -c = 0.99 and 0.95. Be patient, wait for the analysis to finish.

[Dateline]

So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little bit has been done.

[weidonglu]

The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome sequences in my case, the run ends in 5-10 minutes when -c=0.95, and 6-10 h when -c=0.90. 18 GB of data is too large for cd-hit-est!