arpcard/rgi

RGI heatmap does not execute

DeepakNandi opened this issue · 5 comments

DeepakNandi commented

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):

  • OS: LINUX
  • Browser :chrome
raphenya commented

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

DeepakNandi commented

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

@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 commented

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