Trinity assembly and ORF decoder issue

Question

[onspotproductions]

I assembled some transcripts using trinity and now would like to find the ORF using transdecoder. I install all the dependencies, but am getting this error when I try to run the predict tool. I ran it as sudo and even checked that the executable was in the correct place.

CMD: /Users/evanclark/Dropbox/Mari/TransDecoder/util/get_top_longest_fasta_entries.pl Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds 5000 > Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000
CMD: ../Cellar/cd-hit/4.6.4/bin/cd-hit-est -r 1 -i Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -c 0.80 -o Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr80 -M 0
Can't exec "../Cellar/cd-hit/4.6.4/bin/cd-hit-est": No such file or directory at ./TransDecoder.Predict line 289.
Error, cmd: ../Cellar/cd-hit/4.6.4/bin/cd-hit-est -r 1 -i Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 -c 0.80 -o Cone_Snail_Assembly_2016.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr80 -M 0 died with ret -1 at ./TransDecoder.Predict line 292.

Answer 1

[EVR]

HI,

Did you install CD-Hit and make sure it is in Home Path?

[onspotproductions]

Yes that was the issue. I installed CD hit in the root install directory, not the directory where the tool was.