Which import method to use for files in format R1, R2, I1, I2


I have some raw fastq files that I just got back and I sent them to a different core this time so I was not familiar with the files formats which look like this:


Each sample has four files, and I wasn’t sure which import method to use since none of them seem to fit this file format.

I am using QIIME version 2019.10

I was using the EMP protocol multiplexed paired-end fastq for data importing.
This is the code I was running earlier:

(qiime2-2019.10) [[email protected] marm]$ qiime tools import \

–type MARMPairedEndSequences
–input-path fastq
–output-path marmot-paired-end-sequences.qza

And then the following error:

/u/local/apps/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/ijson/backends/init.py:21: UserWarning: Cannot determine yajl version, assuming <1.0.12
warnings.warn(‘Cannot determine yajl version, assuming <1.0.12’)
Traceback (most recent call last):
File “/u/local/apps/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 158, in import_data
File “/u/local/apps/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 213, in import_data
output_dir_fmt = pm.get_directory_format(type_)
File “/u/local/apps/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 157, in get_directory_format
% semantic_type)
TypeError: Semantic type MARMPairedEndSequences does not have a compatible directory format.

An unexpected error has occurred:

Semantic type MARMPairedEndSequences does not have a compatible directory format.

Am I using the wrong import method?

Thank you!!!

1 Like

try this, it worked for me, BUT before you have to:

  • delete all _I_files and put the other files in the FOLDER
    then it should work
    qiime tools import
    –type ‘SampleData[PairedEndSequencesWithQuality]’
    –input-path FOLDER/
    –input-format CasavaOneEightSingleLanePerSampleDirFmt
    –output-path demux-paired-end.qza
1 Like

Hi @ginajohnson!

I’m not sure what @rotifer is showing you here, QIIME 2 doesn’t currently have a dual-index EMP-style format - you will need to find a way to demultiplex these data outside of QIIME 2 and then import the demultiplexed reads. Sorry for the hassle!

PS - where did you come up with this type?

Did you find that out in the wild somewhere? To the best of my knowledge no plugin in the QIIME 2 ecosystem defines a type with that name, so just curious to know if its a typo, or if it has some specific meaning - please let us know, that way if we ever decide to add this type we can consider this name.

Ok. Thank you for the reply! Sorry the type I put is an error!

1 Like

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