It looks to me that TransDecoder cannot be found, based on the error message highlighted in bold, which is strange because I understand that a new conda environment will be created to install the necessary programs. I have confirmed that the input files are indeed in $PWD. I have tried searching for "TransDecoder.LongOrfs" in all condaEnv directories in TransPi, and true enough, I cannot find the script in any of the condaEnv bins. Could it be that the conda create command was not executed? I have also tried installing TransDecoder and added it to $PATH, but even then, the program still cannot be found by TransPi. Is there a way to resolve this? Or can I perhaps install the condaEnv on my own before resuming the run? I need advice on how the condaEnvs are named as they seem pretty random. How would I need to name it so that nextflow will know to activate that particular environment for TransDecoder-related programs?
Hi @rivera10
Thank you for creating the TransPi pipeline. I have tried running it and encountered this error:
=============================================================================================== "Something went wrong. Check error message below and/or log files. Error executing process > 'transdecoder_longorf (GER921R_trimmed_corr)'
Caused by: Process
transdecoder_longorf (GER921R_trimmed_corr)terminated with an error exit status (127)Command executed:
cp GER921R_trimmed_corr.combined.okay.fa GER921R_trimmed_corr_asssembly.fasta
echo -e "\n-- TransDecoder.LongOrfs... --\n"
TransDecoder.LongOrfs -t GER921R_trimmed_corr.combined.okay.fa --output_dir GER921R_trimmed_corr.transdecoder_dir -G Universal
cp GER921R_trimmed_corr.transdecoder_dir/longest_orfs.pep GER921R_trimmed_corr.longest_orfs.pep
echo -e "\n-- Done with TransDecoder.LongOrfs --\n"
v=$( TransDecoder.LongOrfs --version | cut -f 2 -d " " ) echo "Transdecoder: $v" >transdecoder.version.txt
Command exit status: 127
Command output:
-- TransDecoder.LongOrfs... --
Command error: .command.sh: line 6: TransDecoder.LongOrfs: command not found
Work dir: ~/Applications/TransPi/working_RNA_combined/58/d62e3e4699b1267a0b39d17184c8bf
Tip: when you have fixed the problem you can continue the execution adding the option
-resumeto the run command line"===============================================================================================
It looks to me that TransDecoder cannot be found, based on the error message highlighted in bold, which is strange because I understand that a new conda environment will be created to install the necessary programs. I have confirmed that the input files are indeed in $PWD. I have tried searching for "TransDecoder.LongOrfs" in all condaEnv directories in TransPi, and true enough, I cannot find the script in any of the condaEnv bins. Could it be that the conda create command was not executed? I have also tried installing TransDecoder and added it to $PATH, but even then, the program still cannot be found by TransPi. Is there a way to resolve this? Or can I perhaps install the condaEnv on my own before resuming the run? I need advice on how the condaEnvs are named as they seem pretty random. How would I need to name it so that nextflow will know to activate that particular environment for TransDecoder-related programs?
Kindly advise, thank you!
Regards Marc