using output reCOgnizer... error

[vicru93]

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

[vicru93]

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 main() File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 679, in main taxon_to_mmap_to_orthologs = download_resources( File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 570, in download_resources kegg_prefixes = [(taxon, taxon2prefix(taxon, taxa_df)) for taxon in taxa] File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 570, in kegg_prefixes = [(taxon, taxon2prefix(taxon, taxa_df)) for taxon in taxa] File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 519, in taxon2prefix if taxon_name.split(' (')[0] in organism_df.index: # Homo sapiens (human) -> Homo sapiens AttributeError: 'float' object has no attribute 'split'

[iquasere]

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.

[vicru93]

¡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, -qcolrecibe como parámetro una lista de columnas separadas por comas en su conjunto de datos de entrada con valores de cuantificación; si no está disponible, -iqse 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:

[iquasere]

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.

[vicru93]

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

[vicru93]

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 Checking on [1] KGMLs for taxon [ko]: 100%|==============================================================================================================| 1/1 [00:00<00:00, 22.67it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.48it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 141.29it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 130.38it/s] Checking on [1] KGMLs for taxon [hpy]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 56.05it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.04it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.11it/s] Checking on [1] KGMLs for taxon [ctr]: 100%|============================================================================================================| 1/1 [00:00<00:00, 222.46it/s] Checking on [1] KGMLs for taxon [ebf]: 100%|============================================================================================================| 1/1 [00:00<00:00, 217.76it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.52it/s] Checking on [1] KGMLs for taxon [ko]: 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100%|=============================================================================================================| 1/1 [00:00<00:00, 20.28it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 147.24it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.30it/s] Checking on [1] KGMLs for taxon [tpa]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 66.50it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.82it/s] Checking on [1] KGMLs for taxon [ko]: 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100%|============================================================================================================| 1/1 [00:00<00:00, 173.52it/s] Checking on [1] KGMLs for taxon [lil]: 100%|============================================================================================================| 1/1 [00:00<00:00, 215.42it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 127.05it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 122.39it/s] Checking on [1] KGMLs for taxon [mtu]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 26.21it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.81it/s] Checking on [1] KGMLs for taxon [lmo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 56.19it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.82it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 141.20it/s] Checking on [1] KGMLs for taxon [ade]: 100%|============================================================================================================| 1/1 [00:00<00:00, 190.92it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 142.98it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 137.51it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.09it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 137.75it/s] Checking on [1] KGMLs for taxon [spy]: 100%|============================================================================================================| 1/1 [00:00<00:00, 208.28it/s] Checking on [1] KGMLs for taxon [sau]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 80.50it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 120.23it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.63it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.13it/s] Checking on [1] KGMLs for taxon [cpe]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 23.67it/s] Checking on [1] KGMLs for taxon [cbaf]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 224.86it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.48it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.26it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.86it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.14it/s] Checking on [1] KGMLs for taxon [sau]: 100%|============================================================================================================| 1/1 [00:00<00:00, 225.56it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.89it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.71it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 137.58it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 114.79it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.62it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.87it/s] Checking on [1] KGMLs for taxon [mtu]: 100%|============================================================================================================| 1/1 [00:00<00:00, 202.60it/s] Checking on [1] KGMLs for taxon [cac]: 100%|============================================================================================================| 1/1 [00:00<00:00, 208.09it/s] Checking on [1] KGMLs for taxon [cdf]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 94.37it/s] Checking on [1] KGMLs for taxon [dsy]: 100%|============================================================================================================| 1/1 [00:00<00:00, 207.67it/s] Checking on [1] KGMLs for taxon [csc]: 100%|============================================================================================================| 1/1 [00:00<00:00, 185.07it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.21it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 146.10it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 145.50it/s] Checking on [1] KGMLs for taxon [hpy]: 100%|============================================================================================================| 1/1 [00:00<00:00, 193.30it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.25it/s] Checking on [1] KGMLs for taxon [cje]: 100%|============================================================================================================| 1/1 [00:00<00:00, 233.73it/s] Checking on [1] KGMLs for taxon [tac]: 100%|============================================================================================================| 1/1 [00:00<00:00, 203.76it/s] Checking on [1] KGMLs for taxon [pto]: 100%|============================================================================================================| 1/1 [00:00<00:00, 209.05it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.22it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 122.41it/s] Checking on [1] KGMLs for taxon [rbt]: 100%|============================================================================================================| 1/1 [00:00<00:00, 219.02it/s] Checking on [1] KGMLs for taxon [sml]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 46.66it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 124.03it/s] Checking on [1] KGMLs for taxon [spn]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 37.53it/s] Checking on [1] KGMLs for taxon [mab]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 28.93it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.38it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 139.34it/s] Checking on [1] KGMLs for taxon [tar]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 46.41it/s] Checking on [1] KGMLs for taxon [ots]: 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100%|=============================================================================================================| 1/1 [00:00<00:00, 133.49it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 124.29it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 128.72it/s] Checking on [1] KGMLs for taxon [vfi]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 59.37it/s] Checking on [1] KGMLs for taxon [aha]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 53.29it/s] Checking on [1] KGMLs for taxon [vch]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 51.77it/s] Checking on [1] KGMLs for taxon [bbag]: 100%|============================================================================================================| 1/1 [00:00<00:00, 49.20it/s] Checking on [1] KGMLs for taxon [xcc]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 43.04it/s] Checking on [1] KGMLs for taxon [mth]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 40.33it/s] Checking on [1] KGMLs for taxon [bbau]: 100%|============================================================================================================| 1/1 [00:00<00:00, 49.26it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 121.51it/s] Checking on [1] KGMLs for taxon [ljo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 45.18it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 128.58it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 128.14it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 137.36it/s] Checking on [1] KGMLs for taxon [spy]: 100%|============================================================================================================| 1/1 [00:00<00:00, 207.88it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 139.56it/s] Checking on [1] KGMLs for taxon [tma]: 100%|============================================================================================================| 1/1 [00:00<00:00, 229.22it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.77it/s] Checking on [1] KGMLs for taxon [ret]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 52.06it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 150.63it/s] Checking on [1] KGMLs for taxon [cbo]: 100%|============================================================================================================| 1/1 [00:00<00:00, 206.41it/s] Checking on [1] KGMLs for taxon [kox]: 100%|============================================================================================================| 1/1 [00:00<00:00, 200.15it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 128.29it/s] Checking on [1] KGMLs for taxon [mpd]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 59.91it/s] Checking on [1] KGMLs for taxon [pae]: 100%|============================================================================================================| 1/1 [00:00<00:00, 224.26it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 122.47it/s] Checking on [1] KGMLs for taxon [tpa]: 100%|============================================================================================================| 1/1 [00:00<00:00, 205.59it/s] Checking on [1] KGMLs for taxon [mse]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 10.69it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.00it/s] Checking on [1] KGMLs for taxon [rbm]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 64.71it/s] Checking on [1] KGMLs for taxon [enc]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 64.23it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.02it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.67it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.09it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 139.39it/s] Checking on [1] KGMLs for taxon [efa]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 42.81it/s] Checking on [1] KGMLs for taxon [sdl]: 100%|============================================================================================================| 1/1 [00:00<00:00, 216.95it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 127.13it/s] Checking on [1] KGMLs for taxon [bacc]: 100%|============================================================================================================| 1/1 [00:00<00:00, 46.21it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.53it/s] Checking on [1] KGMLs for taxon [lla]: 100%|============================================================================================================| 1/1 [00:00<00:00, 220.47it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.59it/s] Checking on [1] KGMLs for taxon [bce]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 47.49it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.24it/s] Checking on [1] KGMLs for taxon [bla]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 63.09it/s] Checking on [1] KGMLs for taxon [beb]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 85.99it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 123.45it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.93it/s] Checking on [1] KGMLs for taxon [mif]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 43.44it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.48it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.36it/s] Checking on [1] KGMLs for taxon [blo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 39.18it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.38it/s] Checking on [1] KGMLs for taxon [buc]: 100%|============================================================================================================| 1/1 [00:00<00:00, 212.55it/s] Checking on [1] KGMLs for taxon [mmp]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 65.01it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.28it/s] Checking on [1] KGMLs for taxon [afu]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 54.92it/s] Checking on [1] KGMLs for taxon [acb]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 76.42it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.32it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 137.67it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.19it/s] Checking on [1] KGMLs for taxon [mmp]: 100%|============================================================================================================| 1/1 [00:00<00:00, 180.18it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.25it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.35it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 145.78it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.76it/s] Checking on [1] KGMLs for taxon [pcop]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 206.39it/s] Checking on [1] KGMLs for taxon [son]: 100%|============================================================================================================| 1/1 [00:00<00:00, 209.28it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 130.48it/s] Checking on [1] KGMLs for taxon [pnv]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 48.50it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 139.14it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.20it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 143.34it/s] Checking on [1] KGMLs for taxon [pac]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 65.89it/s] Checking on [1] KGMLs for taxon [faq]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 60.67it/s] Checking on [1] KGMLs for taxon [ko]: 100%|==============================================================================================================| 1/1 [00:00<00:00, 4.41it/s] Checking on [1] KGMLs for taxon [ilo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 44.58it/s] Checking on [1] KGMLs for taxon [pha]: 100%|============================================================================================================| 1/1 [00:00<00:00, 182.10it/s] Checking on [1] KGMLs for taxon [cvi]: 100%|============================================================================================================| 1/1 [00:00<00:00, 201.06it/s] Checking on [1] KGMLs for taxon [mba]: 100%|============================================================================================================| 1/1 [00:00<00:00, 154.03it/s] Checking on [1] KGMLs for taxon [fra]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 49.02it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.43it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 142.10it/s] Checking on [1] KGMLs for taxon [acb]: 100%|============================================================================================================| 1/1 [00:00<00:00, 204.64it/s] Checking on [1] KGMLs for taxon [rbx]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 93.30it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 130.58it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.32it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.89it/s] Checking on [1] KGMLs for taxon [lmo]: 100%|============================================================================================================| 1/1 [00:00<00:00, 221.08it/s] 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] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 141.20it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.88it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.76it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 124.63it/s] Checking on [1] KGMLs for taxon [lme]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 22.00it/s] Checking on [1] KGMLs for taxon [lca]: 100%|============================================================================================================| 1/1 [00:00<00:00, 250.54it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 143.09it/s] Checking on [1] KGMLs for taxon [xfa]: 100%|============================================================================================================| 1/1 [00:00<00:00, 209.93it/s] Checking on [1] KGMLs for taxon [bbs]: 100%|============================================================================================================| 1/1 [00:00<00:00, 199.43it/s] Checking on [1] KGMLs for taxon [det]: 100%|============================================================================================================| 1/1 [00:00<00:00, 192.74it/s] Checking on [1] KGMLs for taxon [pmr]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 44.83it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.25it/s] Checking on [1] KGMLs for taxon [tdn]: 100%|============================================================================================================| 1/1 [00:00<00:00, 225.57it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 138.34it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.14it/s] Checking on [1] KGMLs for taxon [pal]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 65.73it/s] Checking on [1] KGMLs for taxon [efa]: 100%|============================================================================================================| 1/1 [00:00<00:00, 212.19it/s] 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] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 133.79it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 128.39it/s] Checking on [1] KGMLs for taxon [tko]: 100%|============================================================================================================| 1/1 [00:00<00:00, 218.85it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.32it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.24it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.39it/s] Checking on [1] KGMLs for taxon [bhe]: 100%|============================================================================================================| 1/1 [00:00<00:00, 200.72it/s] Checking on [1] KGMLs for taxon [bpe]: 100%|============================================================================================================| 1/1 [00:00<00:00, 241.62it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 124.98it/s] Checking on [1] KGMLs for taxon [rpa]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 36.98it/s] Checking on [1] KGMLs for taxon [acop]: 100%|============================================================================================================| 1/1 [00:00<00:00, 41.27it/s] Checking on [1] KGMLs for taxon [pom]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 63.47it/s] Checking on [1] KGMLs for taxon [bps]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 61.95it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 127.13it/s] Checking on [1] KGMLs for taxon [msm]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 59.66it/s] Checking on [1] KGMLs for taxon [kpn]: 100%|============================================================================================================| 1/1 [00:00<00:00, 222.30it/s] Checking on [1] KGMLs for taxon [metb]: 100%|============================================================================================================| 1/1 [00:00<00:00, 61.68it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 142.93it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.44it/s] Checking on [1] KGMLs for taxon [mja]: 100%|============================================================================================================| 1/1 [00:00<00:00, 181.58it/s] Checking on [1] KGMLs for taxon [msi]: 100%|============================================================================================================| 1/1 [00:00<00:00, 155.92it/s] Checking on [1] KGMLs for taxon [rsc]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 56.61it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.21it/s] Checking on [1] KGMLs for taxon [cpn]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 7.73it/s] Checking on [1] KGMLs for taxon [mvo]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 19.19it/s] Checking on [1] KGMLs for taxon [cff]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 58.66it/s] Checking on [1] KGMLs for taxon [ko]: 100%|==============================================================================================================| 1/1 [00:00<00:00, 7.84it/s] Checking on [1] KGMLs for taxon [bsun]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 213.95it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 135.43it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.54it/s] Checking on [1] KGMLs for taxon [eca]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 65.36it/s] Checking on [1] KGMLs for taxon [ppr]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 72.65it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 148.73it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.11it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 145.37it/s] Checking on [1] KGMLs for taxon [salb]: 100%|============================================================================================================| 1/1 [00:00<00:00, 81.88it/s] Checking on [1] KGMLs for taxon [cco]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 90.77it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.88it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 139.75it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.97it/s] Checking on [1] KGMLs for taxon [eam]: 100%|============================================================================================================| 1/1 [00:00<00:00, 218.40it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.72it/s] Checking on [1] KGMLs for taxon [rrs]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 65.44it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.65it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 134.61it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.02it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.31it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 141.02it/s] Checking on [1] KGMLs for taxon [cbu]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 51.83it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.88it/s] Checking on [1] KGMLs for taxon [shi]: 100%|============================================================================================================| 1/1 [00:00<00:00, 222.37it/s] Checking on [1] KGMLs for taxon [ele]: 100%|============================================================================================================| 1/1 [00:00<00:00, 227.00it/s] Checking on [1] KGMLs for taxon [lpse]: 100%|============================================================================================================| 1/1 [00:00<00:00, 38.12it/s] Checking on [1] KGMLs for taxon [bme]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 72.26it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 122.60it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.69it/s] Checking on [1] KGMLs for taxon [saes]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 180.35it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 116.68it/s] Checking on [1] KGMLs for taxon [pst]: 100%|============================================================================================================| 1/1 [00:00<00:00, 188.96it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.19it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 131.81it/s] Checking on [1] KGMLs for taxon [afr]: 100%|============================================================================================================| 1/1 [00:00<00:00, 192.33it/s] Checking on [1] KGMLs for taxon [xbo]: 100%|============================================================================================================| 1/1 [00:00<00:00, 206.58it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.57it/s] Checking on [1] KGMLs for taxon [git]: 100%|============================================================================================================| 1/1 [00:00<00:00, 193.46it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 132.20it/s] Checking on [1] KGMLs for taxon [rcp]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 45.11it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 118.87it/s] Checking on [1] KGMLs for taxon [mbac]: 100%|============================================================================================================| 1/1 [00:00<00:00, 62.18it/s] Checking on [1] KGMLs for taxon [pae]: 100%|============================================================================================================| 1/1 [00:00<00:00, 192.13it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 117.10it/s] Checking on [1] KGMLs for taxon [este]: 100%|===========================================================================================================| 1/1 [00:00<00:00, 206.26it/s] Checking on [1] KGMLs for taxon [bfr]: 100%|============================================================================================================| 1/1 [00:00<00:00, 181.22it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 136.23it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 145.12it/s] Checking on [1] KGMLs for taxon [sds]: 100%|============================================================================================================| 1/1 [00:00<00:00, 188.40it/s] Checking on [1] KGMLs for taxon [cbe]: 100%|============================================================================================================| 1/1 [00:00<00:00, 251.58it/s] Checking on [1] KGMLs for taxon [lac]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 47.73it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 129.89it/s] Checking on [1] KGMLs for taxon [nmr]: 100%|============================================================================================================| 1/1 [00:00<00:00, 225.37it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 123.15it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 126.14it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 125.19it/s] Checking on [1] KGMLs for taxon [ko]: 100%|==============================================================================================================| 1/1 [00:00<00:00, 8.43it/s] Checking on [1] KGMLs for taxon [htu]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 53.11it/s] Checking on [1] KGMLs for taxon [ko]: 100%|=============================================================================================================| 1/1 [00:00<00:00, 140.84it/s] 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 main() File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 704, in main chart_map( File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/bin/keggcharter", line 654, in chart_map kegg_pathway_map.genomic_potential_taxa( File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/share/keggpathway_map.py", line 369, in genomic_potential_taxa taxa = self.most_abundant_taxa(data, samples, taxa_column, number_of_taxa=number_of_taxa) File "/hpcfs/home/ing_quimica/v.rua/.conda/envs/KEGG_CH/share/keggpathway_map.py", line 342, in most_abundant_taxa data = data.groupby(taxa_column)[columns].sum().sum(axis=1).sort_values(ascending=False) File "/hpcfs/home/ing_quimica/v.rua/.local/lib/python3.10/site-packages/pandas/core/groupby/generic.py", line 1338, in getitem return super().getitem(key) File "/hpcfs/home/ing_quimica/v.rua/.local/lib/python3.10/site-packages/pandas/core/base.py", line 250, in getitem raise KeyError(f"Column not found: {key}") KeyError: 'Column not found: None'

[iquasere]

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.

[vicru93]

Thanks for your help, I can now get my results