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EBI-Metagenomics / emg-toolkit

MGnify API toolkit
https://www.ebi.ac.uk/metagenomics
Apache License 2.0
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mg-toolkit for confidential MGnify study #6

Closed jmcelh closed 4 years ago

jmcelh commented 5 years ago

Dear Ola,

I would like to try out the mg-toolkit for retrieving the metadata etc. for our team's study, ERP116156, (I am following the tutorials we learnt at EMBL metagenomics bioinformatics 2018) but receive a traceback error (please see attached metadata_error.txt) when trying the command:

$ mg-toolkit original_metadata -a ERP116156

With the bulk download command the result is no retrieved files but otherwise a standard looking output (please see bulk.txt attached)

I suspect that this might be due to my study being listed as confidential at present (the command appears to work fine on a public study), if this is the case, might there be a workaround (asides from making it public just yet)?

Any advice would be most appreciated.

Best wishes,

James

P.S. I am not sure if this constitutes an issue with the package per se and apologize if this is not the forum for such an post (I am new to github).

metadata_error.txt bulk.txt

lambros-f commented 4 years ago

Hey jmcelh

Did you ever figure out what the error is with this?

I am having the same issue but for public studies

mberacochea commented 4 years ago

Keep in mind that the toolkit doesn't support private (confidential) data sets at the moment . I've created a ticket to support private data sets https://github.com/EBI-Metagenomics/emg-toolkit/issues/10 but I can't provide an ETA.

There is a new version available that fixes this problem. Thank you for reporting the bug.