Closed vicru93 closed 7 months ago
keggcharter -f reCOGnizer_results.tsv -o keggcharter_output -ecc 'EC number' -koc 'KO' -tc 'taxonomic_range_name' -mm "00680" -qcol 'bitscore' -dq --include-missing-genomes
2024-01-09 21:36:43: Reading input data.
Created keggcharter_output/maps
Created keggcharter_output/tsvs
2024-01-09 21:37:08: Arguments valid.
Converting 1200 KOs to EC numbers through the KEGG API: 100%|==========================================================================================| 30/30 [00:42<00:00, 1.40s/it]
Converting 756 EC numbers to KOs through the KEGG API: 100%|===========================================================================================| 19/19 [00:27<00:00, 1.47s/it]
Converting 1477 EC numbers to KOs through the KEGG API: 100%|==========================================================================================| 37/37 [00:52<00:00, 1.42s/it]
Converting 3320 KOs to EC numbers through the KEGG API: 100%|==========================================================================================| 83/83 [01:57<00:00, 1.41s/it]
2024-01-09 21:43:56: Saving new information to: keggcharter_output/KEGGCharter_results.tsv
2024-01-09 21:45:20: Data prepared for charting.
2024-01-09 21:52:10: Downloading resources
2024-01-09 21:52:11: Obtaining KEGG prefixes from inputted taxa
Traceback (most recent call last):
File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 722, in
Hey there! Could you please share the input you are giving KEGGCharter? The fact that KEGGCharter fails without more information shouldn't happen, I want to see what taxa is involved here.
I also see some erroneous inputs through the command line, e.g., -qcol
receives as parameter a comma-separated list of columns in your input dataset with quantification values, if it's not available the -iq
parameter can be used. After I see what's going on, I'll send a command with the right format.
¡Hola! ¿Podrías compartir la información que estás dando a KEGGCharter? El hecho de que KEGGCharter falle sin más información no debería suceder; quiero ver qué taxones están involucrados aquí.
También veo algunas entradas erróneas a través de la línea de comando, por ejemplo,
-qcol
recibe como parámetro una lista de columnas separadas por comas en su conjunto de datos de entrada con valores de cuantificación; si no está disponible,-iq
se puede usar el parámetro. Después de ver qué está pasando, enviaré un comando con el formato correcto.
Hello, thanks for answering:
I would like to briefly explain my project... I am working with metagenomic samples from microbiomes related to anaerobic digestion processes, so I want to represent my kegg maps at a taxonomic level, for this I used "reCOgnizer" to obtain the input for Keggcharter using the map -mm "00680".
I have had some problems using this tool, I still don't understand some variables, could you help me with this, please?
I share with you the link where you can find all the files that I obtained with reCOgnizer when using it with one of my samples, I will be attentive to your response:
The error was reproducible on my end. It seems that taxa != np.nan
no longer works for detecting the nan
values of pandas... better to just do a type(taxa) == str
. This fixed the bug reported here, and will be included in KEGGCharter 1.1.2
, which will be available through Bioconda in a few minutes.
About the command:
keggcharter -f reCOGnizer_results.tsv -o keggcharter_output -ecc 'EC number' -koc 'KO' -tc 'taxonomic_range_name' -mm "00680" -qcol 'bitscore' -dq --include-missing-genomes
The only wrong value is really on the -qcol 'bitscore'
part. Bitscore is related to the e-values in considering the quality of annotation matches. Since you have no quantification in your input dataset, you can simply use the -iq
flag, which will create a mock column, Quantification (KEGGCharter)
, where all rows are given the value of 1. The command then becomes:
keggcharter -f reCOGnizer_results.tsv -o keggcharter_output -ecc 'EC number' -koc 'KO' -tc 'taxonomic_range_name' -mm "00680" -iq -dq --include-missing-genomes
reCOGnizer also outputs COG information, and if you used the COG report it outputs (COG_report.tsv
), this information could be used in KEGGCharter using the -cogc 'DB ID'
parameter.
Hello:
I'm still having problems getting results using the output of recognizer
I also tried using UPIMAPI, but unfortunately it always tells me that I have problems with my memory resources.
command line (UPIMAPI): upimapi -i /hpcfs/home/ing_quimica/v.rua/anotaciones/predicted_proteins_A14.faa -o hpcfs/home/ing_quimica/v.rua/anotaciones/A14 -t 100 --columns "Taxonomic lineage IDs (SPECIES)" max-memory 140 --diamond-mode ultra_sensitive -b 25
I don't know if it's a problem in the way I'm using reCOgnizer, this was the command line I used:
recognizer -f /hpcfs/home/ing_quimica/v.rua/anotaciones/predicted_proteins_A2.faa -o hpcfs/home/ing_quimica/v.rua/anotaciones/recognizer --resources-directory /hpcfs/home/ing_quimica/v.rua/recognizer_database -t 80
Sorry, This is my update:
keggcharter -f reCOGnizer_results.tsv -o keggcharter_output -ecc 'EC number' -koc 'KO' -tc 'taxonomic_range_name' -mm "00680" -dq --include-missing-genomes -t 100
2024-01-11 21:07:10: Reading input data.
Created keggcharter_output/maps
Created keggcharter_output/tsvs
2024-01-11 21:07:36: Arguments valid.
Converting 1200 KOs to EC numbers through the KEGG API: 100%|==========================================================================================| 30/30 [00:42<00:00, 1.41s/it]
Converting 756 EC numbers to KOs through the KEGG API: 100%|===========================================================================================| 19/19 [00:27<00:00, 1.43s/it]
Converting 1477 EC numbers to KOs through the KEGG API: 100%|==========================================================================================| 37/37 [00:52<00:00, 1.42s/it]
Converting 3316 KOs to EC numbers through the KEGG API: 100%|==========================================================================================| 83/83 [01:54<00:00, 1.38s/it]
2024-01-11 21:14:10: Saving new information to: keggcharter_output/KEGGCharter_results.tsv
2024-01-11 21:15:05: Preparing data for charting.
2024-01-11 21:15:29: Saving data for charting.
2024-01-11 21:22:08: Downloading resources
2024-01-11 21:22:08: Obtaining KEGG prefixes from inputted taxa
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Checking on [1] KGMLs for taxon [rbx]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 93.30it/s]
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Checking on [1] KGMLs for taxon [mark]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 179.16it/s]
Checking on [1] KGMLs for taxon [abi]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 40.16it/s]
Checking on [1] KGMLs for taxon [sco]: 100%|============================================================================================================| 1/1 [00:00<00:00, 191.19it/s]
Checking on [1] KGMLs for taxon [eco]: 100%|============================================================================================================| 1/1 [00:00<00:00, 181.20it/s]
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Checking on [1] KGMLs for taxon [det]: 100%|============================================================================================================| 1/1 [00:00<00:00, 192.74it/s]
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Checking on [1] KGMLs for taxon [ges]: 100%|============================================================================================================| 1/1 [00:00<00:00, 201.66it/s]
Checking on [1] KGMLs for taxon [ant]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 59.00it/s]
Checking on [1] KGMLs for taxon [nis]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 47.10it/s]
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Checking on [1] KGMLs for taxon [mvo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 19.19it/s]
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Checking on [1] KGMLs for taxon [ele]: 100%|============================================================================================================| 1/1 [00:00<00:00, 227.00it/s]
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Checking on [1] KGMLs for taxon [git]: 100%|============================================================================================================| 1/1 [00:00<00:00, 193.46it/s]
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Checking on [1] KGMLs for taxon [lac]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 47.73it/s]
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Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 145.45it/s]
Checking on [1] KGMLs for taxon [cch]: 100%|============================================================================================================| 1/1 [00:00<00:00, 226.94it/s]
Checking on [1] KGMLs for taxon [cph]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 30.12it/s]
Checking on [1] KGMLs for taxon [plt]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 47.04it/s]
Checking on [1] KGMLs for taxon [cch]: 100%|============================================================================================================| 1/1 [00:00<00:00, 198.06it/s]
Checking on [1] KGMLs for taxon [bpen]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 235.82it/s]
Checking on [1] KGMLs for taxon [pgi]: 100%|============================================================================================================| 1/1 [00:00<00:00, 193.15it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.20it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.23it/s]
Checking on [1] KGMLs for taxon [kpn]: 100%|============================================================================================================| 1/1 [00:00<00:00, 186.62it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.07it/s]
Checking on [1] KGMLs for taxon [nfa]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 34.73it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 122.80it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.14it/s]
Checking on [1] KGMLs for taxon [psyt]: 100%|============================================================================================================| 1/1 [00:00<00:00, 58.64it/s]
Checking on [1] KGMLs for taxon [fpr]: 100%|============================================================================================================| 1/1 [00:00<00:00, 174.29it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 130.56it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.10it/s]
Checking on [1] KGMLs for taxon [ecas]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 202.83it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 118.43it/s]
Checking on [1] KGMLs for taxon [hnv]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 64.01it/s]
Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 124.95it/s]
Getting information for 341 taxa: 100%|==============================================================================================================| 342/342 [03:53<00:00, 1.46it/s]
2024-01-11 21:26:03: Generated taxon_to_mmap_to_orthologs.json
2024-01-11 21:26:03: Saving taxon_to_mmap_to_orthologs.
2024-01-11 21:26:03: Creating KEGG Pathway representations for 1 metabolic pathways.
2024-01-11 21:26:03: [1/1] Methane metabolism
Traceback (most recent call last):
File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 733, in
Since you have no quantification in your input dataset, you can simply use the -iq flag, which will create a mock column, Quantification (KEGGCharter), where all rows are given the value of 1. The command then becomes: keggcharter -f reCOGnizer_results.tsv -o keggcharter_output -ecc 'EC number' -koc 'KO' -tc 'taxonomic_range_name' -mm "00680" -iq -dq --include-missing-genomes
Try using the -iq
flag.
Thanks for your help, I can now get my results
Hello, I am using keggcharter with the "output" that I got from reCOgnizer, but I constantly get errors, could you help me build my command line, please?
This is the command line I am using: keggcharter -f reCOGnizer_results.tsv -ecc 'EC number' -koc 'KO' -o keggcharter_output -it "taxonomic_range_name" -iq -t 90 -mm 00680
These are the headers of the output (reCOGnizer_results.tsv) obtained with reCOgnizer: qseqid DB ID Protein description DB description EC number CDD ID taxonomic_range_name taxonomic_range pident length mismatch gapopen qstart qend sstart send evalue bitscore General functional category Functional category KO