traitar phenotype #71
Comments
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Dear Lan, Thanks for your interest in Traitar. The command to run Traitar using the test data should be something like: Best regards, Aaron |
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Thank you for your timely reply. The previous problem seems to have been solved, but a new error has appeared. |
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I'm sorry to bother you again. According to your suggestion, I first ran traitar pfam --local pfam/, Then run traitar phenotype pfam/ test1/ test1/samples.txt from_nucleotides traitar_test -c 2 --overwrite. This all seems to be ok, only in the last tip traitar phenotype pfam/ test1/ test1/samples.txt from_nucleotides traitar_test -c 2 --overwrite2023-07-26 13:43:33,040 - Running annotate as part of predict The resulting file appears to be faulty. There is still no graph in the final result, but the file's contents are no longer 0. I don't know where the problem is. I hope you can help me solve it, thank you. |
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Generation of the heat map is not supported at the moment unfortunately. You can use the result tables to make your own version. Sorry about that. |
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Ok, thank you for your answer. There is one last problem. Using your example data, there are only phenotypes marked 0 and 3 in the generated Table and flat files（predictions_majority-vote_combined.txt）, without 1 and 2, but there will be 1 and 2 in your running results. I don't know whether it is caused by the different versions of Pfam used, but I am using Pfam35.0 now. Or is it something else?
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Thanks for flagging this. That's not expected. I need to look into it. It should be run on Pfam 27.0. That's what was used to train the models. |
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Hi Lan, I imagine you're using the Traitar3 version through Conda. I found that there is an issue in that version that will mean only the results from the phypat+PGL model will be produced (rather than both phypat and phypat+PGL). At the moment the only fix is to use the original Traitar version if you manage to install it. I will see if this can be sorted out, but this may take a while. |
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Thank you very, very much. Indeed, I use Traitar version 3, and I plan to reinstall the original Traitar version. Thank you very much for your prompt and timely reply, which is of great help to me. |
Dear Aaron Weimann,
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.
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