import BIOM file V100 into QIIME2 error

Hello everyone, I am new to the forum and ran into an error trying to import a BIOM table into QIIME. I reviewed previously asked questions, but wasn’t able to find something similar hence I am asking for help. I am trying to import a BIOM table into QIIME2 using the command line interface. The code is below. I receive an error that I am not sure how to solve. I reviewed the sample BIOM table from the tutorials and the format appears the same, yet I get an error. Any help would be appreciated. Thanks!

Using QIIME2-2019.7 natively installed on macOS Catalina

##import BIOM file

qiime tools import

–input-path RISK_all_samples.biom

–type "FeatureTable[Frequency]

–input-format BIOMV100Format

–output-path /Desktop/output/

##BIOM file header information

{“id”: “None”,“format”: “Biological Observation Matrix 1.0.0”,“format_url”: “”,“type”: “OTU table”,“generated_by”: “BIOM-Format 1.3.1”,“date”: “2016-11-23T05:05:35.155933”,“matrix_type”: “sparse”,“matrix_element_type”: “float”,“shape”: [2064, 929],“data”:

##error message

An unexpected error has occurred:

’FeatureTable[Frequency] --input-format BIOMV100Format --output-path /Desktop/output\nqiime tools import --input-path RISK_all_samples.biom --type FeatureTable[Frequency]’ could not be parsed, it may not be a QIIME 2 type or it may not be an atomic type. Use ast_to_type instead.

Hey @rajesh512!

Welcome to the forum!

It looks like this is a case of “string-quoting” getting out of hand. It looks like one of the options is missing a closing quote:

–type "FeatureTable[Frequency]

This caused the command line to pass all of this as the type:

"FeatureTable[Frequency] --input-format BIOMV100Format --output-path /Desktop/output\nqiime tools import --input-path RISK_all_samples.biom --type FeatureTable[Frequency]"

Which is the cause of the scary error.

Double check that all of your quotation marks start and end where they should and give the command another shot. Let us know how it goes!


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