Error: traitar phenotype

[lanlan0210]

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.

[nick-youngblut]

@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

[lanlan0210]

Thank you for your timely reply. The previous problem seems solved, but a new error has appeared.

Looking forward to your reply.

[evazio]

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.

[mgabriell1]

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'

[nick-youngblut]

@mgabriell1 do you have write permissions to Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/?

[mgabriell1]

Assuming that's the relative path in <out_dir>, yes

[nick-youngblut]

Does Genome00005//traitar_result/phenotypic_predictions/annotation/pfam/ actually exist?

[mgabriell1]

It was created by traitar, but it was empty (hence the error)

[nick-youngblut]

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.

[mgabriell1]

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

[smta11]

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!

[nick-youngblut]

For some reason hmmsearch is not writing an output:

traitar3/traitar/traitar_cls.py

Line 283 in a6d8772

outfile = os.path.join(a_dir, out_samples[i] + '_domtblout.dat')