brianjohnhaas
commented
1 year ago 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
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
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