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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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no such option: --bamsnap #84

Closed hzlnutspread closed 1 year ago

hzlnutspread commented 1 year ago

When I run the tool locally after downloading all of the dependencies manually, I run all of the bash scripts but they all fail with the following error:

x_TEA_main.py: error: no such option: --bamsnap
Usage: x_TEA_main.py [options]

Should I remove this option from the command in the bash files or what should be done to overcome this error?

Thanks

simoncchu commented 1 year ago

yes, please remove this option. It doesn't affect the results.

simoncchu commented 1 year ago

Could you post the content of the generated command file named like run_xTEA_pipeline.sh ?

simoncchu commented 1 year ago

All the commands look good to me. I am not sure where the error was triggered... Are you working on non-human species? Looks like you are working on apple genome. All the annotation files are for human only. Maybe this is the reason.

hzlnutspread commented 1 year ago

yes @simoncchu this is a plant genome. Is there another way to use the annotation files for plant and not human?

simoncchu commented 1 year ago

@hzlnutspread you can try https://github.com/parklab/xTea/issues/20

dongjuleem commented 8 months ago

yes, please remove this option. It doesn't affect the results.

Hello. thanks for great tools. I'm leaving a reply because I want to confirm if I understand correctly. After running sh run_gnrt_pipeline.sh, should I remove the options specified for --bamsnap in L1, Alu, SVA/run_xTEA_pipeline.sh?

simoncchu commented 8 months ago

You can keep it, although it may report some error, but the results will not be affected.