I recently had the technical support at my university download QIIME2 v. 2024.10.1 to our research server. I was using v. 2024.5 the week prior using this exact same command w/ the same manifest file to import my reads:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path manifest.csv --output-path demux --input-format PairedEndFastqManifestPhred33
Now that I have access to 2024.10.1, I had to reimport my reads using the same command and same manifest file, but I receive this error:
Traceback (most recent call last):
File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2024.10.1/lib/python3.10/site-packages/qiime2/sdk/util.py", line 113, in parse_format
format_record = pm.formats[format_str]
KeyError: 'PairedEndFastqManifestPhred33'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2024.10.1/lib/python3.10/site-packages/q2cli/builtin/tools.py", line 852, in _import
artifact = qiime2.sdk.Artifact.import_data(
File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2024.10.1/lib/python3.10/site-packages/qiime2/sdk/result.py", line 303, in import_data
view_type = qiime2.sdk.parse_format(view_type)
File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2024.10.1/lib/python3.10/site-packages/qiime2/sdk/util.py", line 115, in parse_format
raise TypeError("No format: %s" % format_str)
TypeError: No format: PairedEndFastqManifestPhred33
An unexpected error has occurred:
No format: PairedEndFastqManifestPhred33
See above for debug info.
I didn't see any differences in the format/syntax for importing my type of data between the versions 2024.5 and 2024.10.1 from docs.qiime2.org on the Importing data pages. I also tried the command:
qiime tools list-formats --importable
to see the importable formats. This command runs without an error, but no results show.
I have also tried:
changing my manifest.csv into a .tsv
changing my manifest.csv file into this format:
"sample-id,forward-absolute-filepath,reverse-absolute-filepath"
And I have tried PairedEndFastqManifestPhred64 vs PairedEndFastqManifestPhred33V2 vs PairedEndFastqManifestPhred64V2
All of which have returned the same error as above. I am trying to figure out with my uni's support team if this error is a formatting error I am causing or an error with how this version was installed. I have looked through the forum posts involving this error, but they all seem to be regarding formatting which I think I'm doing correctly, but I'm not sure.
Thanks for your help!