importing paired end data with manifest file

Hi ,

When using qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path pe-33-manifest.tsv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2 it gives me this error:

File “/Users/myaccount/miniconda3/envs/qiime2CM/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 91, in parse_format
format_record = pm.formats[format_str]
KeyError: ‘PairedEndFastqManifestPhred33V2’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/myaccount/miniconda3/envs/qiime2CM/lib/python3.5/site-packages/q2cli/tools.py”, line 140, in import_data
view_type=input_format)
File “/Users/myaccount/miniconda3/envs/qiime2CM/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 185, in import_data
view_type = qiime2.sdk.parse_format(view_type)
File “/Users/myaccount/miniconda3/envs/qiime2CM/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 93, in parse_format
raise TypeError(“No format: %s” % format_str)
TypeError: No format: PairedEndFastqManifestPhred33V2

I looked in the forum and try different options with no success. I appreciate your time and help.

Hi @claudia,
It looks like you may be using an older version of QIIME 2, from before the V2 manifest formats were introduced.

What version of QIIME 2 are you running? Running this with the latest version of QIIME 2 should work. If you are using an older version and do not want to install the latest version, you should use the older manifest format and see the tutorials appropriate for that version, e.g.,
https://docs.qiime2.org/2019.1/tutorials/importing/

1 Like

Thank you so much for your help! I installed the latest version and it worked very well.

1 Like