single best ORF per transcript

[SUGAM2001]

Hello Sir, @brianjohnhaas
can you please help me to fix the code for the assembly prediction? I want to pick only the best ORF (not more then one genes for the
same transcript)
TransDecoder.Predict -t trinity_out_dir.Trinity.fasta --single_best_orf -O [output directory path]
Running CMD: /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/util/compute_base_probs.pl trinity_out_dir.Trinity.fasta 0 > /home/phdstudent/MSC_Data/Trim/sortme_data/trinity_out_dir.Trinity.fasta.transdecoder_dir/base_freqs.dat

-first extracting base frequencies, we'll need them later.
^CError, cmd: /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/util/compute_base_probs.pl trinity_out_dir.Trinity.fasta 0 > /home/phdstudent/MSC_Data/Trim/sortme_data/trinity_out_dir.Trinity.fasta.transdecoder_dir/base_freqs.dat died with ret 2 No such file or directory at /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/PerlLib/Pipeliner.pm line 185.
Pipeliner::run(Pipeliner=HASH(0x55801e066110)) called at /home/phdstudent/.conda/envs/transdecoder/bin/TransDecoder.LongOrfs line 182

I got this kind of error, can you help me how to fix this?

Thanks

[brianjohnhaas]

hi, it's not finding the file: trinity_out_dir.Trinity.fasta Try providing the full path to it starting from the root / directory.

…

On Thu, Mar 30, 2023 at 2:16 AM SUGAM2001 ***@***.***> wrote: Hello Sir, @brianjohnhaas <https://github.com/brianjohnhaas> can you please help me to fix the code for the assembly prediction? I want to pick only the best ORF (not more then one genes for the same transcript) *TransDecoder.Predict -t trinity_out_dir.Trinity.fasta --single_best_orf -O [output directory path]* Running CMD: /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/util/ compute_base_probs.pl trinity_out_dir.Trinity.fasta 0 > /home/phdstudent/MSC_Data/Trim/sortme_data/trinity_out_dir.Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. ^CError, cmd: /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/util/ compute_base_probs.pl trinity_out_dir.Trinity.fasta 0 > /home/phdstudent/MSC_Data/Trim/sortme_data/trinity_out_dir.Trinity.fasta.transdecoder_dir/base_freqs.dat died with ret 2 No such file or directory at /home/phdstudent/.conda/envs/transdecoder/opt/transdecoder/PerlLib/Pipeliner.pm line 185. Pipeliner::run(Pipeliner=HASH(0x55801e066110)) called at /home/phdstudent/.conda/envs/transdecoder/bin/TransDecoder.LongOrfs line 182 I got this kind of error, can you help me how to fix this? Thanks — Reply to this email directly, view it on GitHub <#173>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX5NPFQLHEIM5757LB3W6UQLPANCNFSM6AAAAAAWMZ6RPE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>