Hello,
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:
UDP0001_S1_L001_I1_001.fastq.gz
UDP0001_S1_L001_I2_001.fastq.gz
UDP0001_S1_L001_R1_001.fastq.gz
UDP0001_S1_L001_R2_001.fastq.gz
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) [ginajohn@n2191 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
view_type=input_format)
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!!!