Semantic type SampleData does not have a compatible directory format.

Technical Support
1

hello,when I am using qiime2.2022.2,I am trying to import a manifest file via the following command
qiime tools import --type 'SampleData[PairedEndsequencesWithQuality]' --input-path UC31manifest.tsv --output-path UC31paired_end_demux.qza --input-format PairedEndFastqManifestPhred33V2
I am receiving the error message blow:
Traceback (most recent call last):
File "/home/zlxgroup/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/zlxgroup/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 277, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/home/zlxgroup/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 293, in _from_view
output_dir_fmt = pm.get_directory_format(type)
File "/home/zlxgroup/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 354, in get_directory_format
raise TypeError(
TypeError: Semantic type SampleData[PairedEndsequencesWithQuality] does not have a compatible directory format.

An unexpected error has occurred:

Semantic type SampleData[PairedEndsequencesWithQuality] does not have a compatible directory format.

See above for debug info.
I am fairly new to bioinformatics so if there is any additional information I can provide to help solve this, please let me know! Thank you.

2

Hello @wwx, it looks like you have a typo. The s in sequences needs to be capitalized. Thank you.

1 Like
5

Thank you very much for you help, It had a new problem when I modified it .
There was a problem importing UC62manifest.tsv:

UC62manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

Filepath on line 1 and column "forward-absolute-filepath" could not be found ($PWD/rawdata/FCAG4GN-NEWwpx150427C-89-29-B_L1_1.fq) for sample "IBD0003UC2".

this is my part of manifest file

UC62manifest.tsv (4.5 KB)

7

Hello @wwx, have you manually verified that the file exists in that location?

1 Like
8

Thank you very much for you help ,but I have question:location which is means the manifest file exists in the PWD folder?
my manifest file and rawdata exist in PWD folder .

9

Does this specific file "$PWD/rawdata/FCAG4GN-NEWwpx150427C-89-29-B_L1_1.fq" exist? That error message is implying that it doesn't.

1 Like
10

hello,Thank you very much fou your help , the file "$PWD/raw data/FCAG4GN-NEWwpx150427C-89-29-B_L1_1.fq" exists, I found that I typed the directory name wrong, the problem has been solved, thank you very much for your answer.

12

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