Question: Trinity assembly and ORF decoder issue
0
gravatar for onspotproductions
4.6 years ago by
United States
onspotproductions140 wrote:

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.

orf rna-seq trinity decoder • 1.8k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by onspotproductions140
1
gravatar for EVR
4.6 years ago by
EVR570
Earth
EVR570 wrote:

HI,

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

ADD COMMENTlink written 4.6 years ago by EVR570
0
gravatar for onspotproductions
4.6 years ago by
United States
onspotproductions140 wrote:

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

ADD COMMENTlink written 4.6 years ago by onspotproductions140
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