Open lanlan0210 opened 1 year ago
@lanlan0210 you are probably not providing all of the required positional arguments:
pfam_dir input_dir sample2file
{from_genes,from_nucleotides,from_annotation_summary}
output_dir
Thank you for your timely reply. The previous problem seems solved, but a new error has appeared. ![Uploading image.png…]() Looking forward to your reply.
Hello,
Same here, I modified the command line as indicated but it gives back this error: FileNotFoundError: [Errno 2] No such file or directory: 'output/annotation/pfam/LBR121___domtblout.dat'
As I understand, this file should be generated by the software. Any ideas on how to solve this? I used the phenotype default traitar phenotype /GENOMICS/genomes/ASSEMBLED/faa/traitar_pfam /GENOMICS/genomes/ASSEMBLED/faa /GENOMICS/genomes/ASSEMBLED/faa/samples.txt from_genes output_traitar
Thank you in advance for the assistance.
Hello, Same problem here. Below you can find the complete log. Thanks in advance for the help!
2023-10-06 13:48:14,059 - Running annotate as part of predict
2023-10-06 13:48:14,060 - Running annotation with hmmer. This step can take a while. A rough estimate for sequential Pfam annotation of genome samples of ~3 Mbs is 10 min per genome.
2023-10-06 13:48:14,062 - Computing hmms
2023-10-06 13:48:14,063 - Using existing file (use --overwrite to recreate): Genome00005//traitar_result/Genome00005.faa
2023-10-06 13:48:14,063 - No. of hmmer commands to run: 0
2023-10-06 13:48:14,063 - Filtering hmm hits
2023-10-06 13:48:14,066 - File doesn't exist, so creating: Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/Genome00005_filtered_best.dat
2023-10-06 13:48:14,066 - No. of hmmer filter commands to run: 1
Traceback (most recent call last):
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/bin/traitar", line 10, in <module>
sys.exit(main())
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/__main__.py", line 101, in main
args.func(args)
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/Commands/phenotype.py", line 34, in phenolyze
p.annotate(args.mode)
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/traitar_cls.py", line 217, in annotate
self.run_hmmer_annotation(self.s2f.loc[:,'sample_file_name'],
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/traitar_cls.py", line 317, in run_hmmer_annotation
fae_func(p)
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/hmmer2filtered_best.py", line 98, in _main_par
main(infile_f, hmm_name, out_best_f)
File "/cluster/project/eawag/p07003/Software/conda/envs/traitar-env/lib/python3.10/site-packages/traitar/hmmer2filtered_best.py", line 110, in main
with open(infile_f) as inF:
FileNotFoundError: [Errno 2] No such file or directory: 'Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/Genome00005_domtblout.dat'
@mgabriell1 do you have write permissions to Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/
?
Assuming that's the relative path in
Does Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/
actually exist?
It was created by traitar, but it was empty (hence the error)
If I had to guess, it could be the quality of your input genome(s). A poor quality genome could result in little or no pfam annotations, which would result in downstream failures of Traitar.
I don't think that's the case. That specific genome has been called as 99.97% complete by CheckM2 so I'd imagine it should be annotated by PFAM. Also this seem to have happened to others, so it's not something that I've only encountered myself
Hello everyone, Has this problem been solved? I am getting the same error with test data and appreciate it if someone shares the solution of this problem. Thanks!
For some reason hmmsearch
is not writing an output: https://github.com/nick-youngblut/traitar3/blob/a6d8772cd8cd62fd7cb63defc37a5c48c974f55f/traitar/traitar_cls.py#L283
Thank you for developing Traitar. I got an error message when I ran the software. The data used is the data in the test file you provided. command: traitar phenotype test samples.txt from_genes output_dir error: usage: traitar phenotype [-h] [-c CPUS] [-x PARALLEL] [-o] [-g {genbank,refseq,img,prodigal,metagenemark}] [-p PRIMARY_MODELS] [-s SECONDARY_MODELS] [-r REARRANGE_HEATMAP] [--no_heatmap_sample_clustering] [--no_heatmap_phenotype_clustering] [-f {png,pdf,svg,jpg}] pfam_dir input_dir sample2file {from_genes,from_nucleotides,from_annotation_summary} output_dir traitar phenotype: error: argument mode: invalid choice: 'output_dir' (choose from 'from_genes', 'from_nucleotides', 'from_annotation_summary'). Can you help me see how to solve it? Looking forward to your reply.