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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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SQMtools subsetTax error #719

Closed mradz19 closed 10 months ago

mradz19 commented 1 year ago

I performed a squeezemeta run and am now trying to analyze the data in R ( I am running the latest versions of both squeezemeta and SQMtools). I used the loadSQM function to import my project as an SQM object, however when running subsetTax I am getting the following error:

bac=subsetTax(new_run, rank="superkingdom", tax="Bacteria", trusted_functions_only=T, ignore_unclassified_functions=T)
Error in subSQM$bins$tax[bins, , drop = FALSE] : subscript out of bounds

I've never had this error before.

fpusan commented 1 year ago

Can you run sqm2zip.py on the project and send the resulting zip file to us?

mradz19 commented 1 year ago

Sure what is the best way to do that? The .zip filder is 4.16GB

fpusan commented 1 year ago

Maybe mega, one drive or something like that?

fpusan commented 10 months ago

Closing due to lack of activity, hope you managed to make it work. Still I wouldn't mind to take a look at that dataset and try to reproduce the error,