Batch export-2020

Continuing the discussion from Batch export for files:
The useful script described previously seems to be incompatible with newer versions of qiime. The following line needs to be adapted -

qiime tools export ${i} --output-dir $output/${i} 

because the currently used ‘input-path’ option will not accept


as an artifact.
Is there a solution or another way to batch export in newer qiime versions?

Many thanks

Hello @shira. What version of QIIME 2 are you using? In the latest versions, you will need to make that line qiime tools export --input-path ${i} --output-path $output/${i}


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Hi @Oddant1, I’m using the last version 2020.8

In that case, I believe changing that line in the way I suggested above will work. Let me know if it doesn’t.

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I am afraid I have tried that and it gave me the following error message:

(1/1?) --input-path option requires an argument

Interesting, did you keep the ${i} after --input-path? Because that is necessary.

Here is the code I ran:

while read i; do
        > echo exporting $i
        qiime tools export --input-path ${I} --output-path $output/${i} 
done < $output/filenames.txt

In the snippet you posted above, you have --input-path ${I} it should be --input-path ${i} with a lowercase i.


Oops! I missed that - thanks so much!
It works very well.

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