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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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RGI heatmap does not execute #266

Closed DeepakNandi closed 1 month ago

DeepakNandi commented 6 months ago

The RGI manual given has a great flaw. It doesnt present the heatmap command. I did follow all the commands in the manual step by step.

Input rgi heatmap -i /home/t7400/json_files -cat drug_class -o rgiheat.png

This folder (containing .json files from rgi main) was used to run heatmap as written in manual/README to generate a result. secondaly, it shows same error when the given command is rgi --version

Error log usage: rgi [] commands are: main Runs rgi application tab Creates a Tab-delimited from rgi results parser Creates categorical .json files RGI wheel visualization. An input .json file containing the RGI results must be input. load Loads CARD database json file clean Removes BLAST databases and temporary files galaxy Galaxy project wrapper database Information on installed card database rgi: error: argument command: invalid choice: 'heatmap' (choose from 'main', 'tab', 'parser', 'load', 'clean', 'galaxy', 'database')

Expected behaviour It was to produce a pie chart of all the correctly found hits and to display it as a file named rgiheat.png

Desktop (please complete the following information):

raphenya commented 5 months ago

@DeepakNandi can you provide all the commands used and version of rgi?

DeepakNandi commented 5 months ago

v 6.0.3 even the .json file formed is over 20MB. Hence not able to visualize in web portal.

Can somebody please explain properly all the coloumns and its significance in the rgi results like ORF_ID | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID |  

Especially these ones: Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family |

Regards and thank you

DeepakNandi commented 4 months ago

@raphenya Can you please explain properly all the coloumns and its significance in the rgi results like ORF_ID | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID |

Especially these ones: Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family |

Regards and thank you

github-actions[bot] commented 2 months ago

Issue is stale and will be closed in 7 days unless there is new activity

agmcarthur commented 3 weeks ago

Full documentation https://github.com/arpcard/rgi