DRAM.py error message for tRNAscan-SE

[Audra-Leigh]

Hello,

I put the following code in: DRAM.py annotate --min_contig_size 1000 --threads 28 -i /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/augustus/21BE/21BE-1000.fasta -o /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/DRAM/21BE-annotation

I would also say that I previously ran this on another file and it successful worked and I was able to distill information from the files.

I get the following error message: Traceback (most recent call last): File "/users/PAS1212/osu10462/miniconda3/bin/DRAM.py", line 7, in exec(compile(f.read(), file, 'exec')) File "/users/PAS1212/osu10462/DRAM/scripts/DRAM.py", line 204, in args.func(*args_dict) File "/users/PAS1212/osu10462/DRAM/mag_annotator/annotate_bins.py", line 1017, in annotate_bins all_annotations = annotate_fastas(fasta_locs, output_dir, db_handler, logger, min_contig_size, prodigal_mode, trans_table, File "/users/PAS1212/osu10462/DRAM/mag_annotator/annotate_bins.py", line 910, in annotate_fastas annotate_fasta(fasta_loc, fasta_name, fasta_dir, db_handler, logger, min_contig_size, prodigal_mode, File "/users/PAS1212/osu10462/DRAM/mag_annotator/annotate_bins.py", line 852, in annotate_fasta trna_table = run_trna_scan(renamed_scaffolds, tmp_dir, fasta_name, logger, threads=threads, verbose=verbose) File "/users/PAS1212/osu10462/DRAM/mag_annotator/annotate_bins.py", line 466, in run_trna_scan run_process(['tRNAscan-SE', '-G', '-o', raw_trnas, '--thread', str(threads), fasta], logger, verbose=verbose) File "/users/PAS1212/osu10462/DRAM/mag_annotator/utils.py", line 61, in run_process results = subprocess.run(command, check=check, shell=shell, File "/users/PAS1212/osu10462/miniconda3/lib/python3.9/subprocess.py", line 505, in run with Popen(popenargs, **kwargs) as process: File "/users/PAS1212/osu10462/miniconda3/lib/python3.9/subprocess.py", line 951, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/users/PAS1212/osu10462/miniconda3/lib/python3.9/subprocess.py", line 1821, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'tRNAscan-SE'

Thanks

Audra

[rmFlynn]

Is tRNAscan-SE installed? How did you install DRAM?

[Audra-Leigh]

I installed DRAM using mamba and so I activate thru mamba activate DRAM. It appears that tRNAscan-SE was not installed so I have installed it manually. That fixed the problem. Thanks!

[rmFlynn]

Excellent, I'm always happy for an easy win. I'm closing this but feel free to open it if you have more problems.