import function not found

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1

Hi I try to import manifest file, metadata, and actual FASTQ files but gets this message that import not found. I use qiime2 2019.7. Thanks

/Users/hebahussein/Desktop/paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2

-bash: import: command not found

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Hi @HebaHussein-1981,

Can you please post your full command and error message? Im guessing you’re either having a command line wrapping issue (wrong \,) or too many or too many spaces.

I’ll just mention that I’m a huge fan of jupyter notebooks for problems like these, because they let you type out and see the whole command at the same time, and you have a record of exactly what you did.

Best,
Justine

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Hi Heba, I echo Justine, you should post your full code and error message -> it may be very simple to correct. Ben

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thanks a lot
/Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

-bash: import: command not found

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thanks ben /Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2
-bash: import: command not found

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image import --type 'SampleData[SingleEndSequencesWithQuality]' --input-path /Users/hebahussein/Desktop/Data/manifest-forward.txt --output-path /Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

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import --type ‘SampleData[SingleEndSequencesWithQuality]’ --input-path /Users/hebahussein/Desktop/Data/manifest-forward.txt --output-path /Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

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Hi @HebaHussein-1981,

It looks like you’re missing the qiime tools portion of the command. All your qiime commands start with qiime and then have a plug-in name.

If you’re not sure about the command or plugin, you can always do something like

qiime --help

which will list all the plug ins. You can also use the tutorials to check what the commands are. I also think you and Ben or Colin worked through how you would load data from a manifest several weeks ago, so double checking that is also an option.

Best,
Justine

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9

Thanks. yes I forgot tools part and I added it. Now, I have a wired error/ debug about semantic output_dir_fmt = pm.get_directory_format(type)

File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 157, in get_directory_format

% semantic_type)

TypeError: Semantic type SampleData[SingleEndSequencesWithQuality] does not have a compatible directory format.

An unexpected error has occurred:

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

See above for debug info.

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10

thanks Ben. i added the import part but got an error related to semantic error output_dir_fmt = pm.get_directory_format(type)

File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 157, in get_directory_format

% semantic_type)

TypeError: Semantic type SampleData[SingleEndSequencesWithQuality] does not have a compatible directory format.

An unexpected error has occurred:

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

See above for debug info.

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11

qiime tools import --type ‘SampleData[SingleEndSequencesWithQuality]’ --input-path /Users/hebahussein/Desktop/Data/manifest-forward.txt --output-path /Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

I think you're trying to mix two different types of import methods - could you describe to us what you're trying to do? We can try to work through it? Also, if you take a look @ the specific parts of the tutorial which are relevant, you will find this code:

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path se-33-manifest
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33V2

Please pay attention to the --type modifier, this would appear different than your code. Ben

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12

Thanks ben. You helped me do analysis for six samples. Now, I try to do for all samples. I try to import individual FASTG, metadata, manifest. – where ok in the terminal but appeared here like this

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qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path /Users/hebahussein/Desktop/Data/manifest-forward.txt --output-path /Users/hebahussein/Desktop/single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

Try this

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thanks ben
ASCII error Error: Detected invalid character in: ‘SampleData[SequencesWithQuality]’

Verify the correct quotes or dashes (ASCII) are being used.

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15

@HebaHussein-1981:

You have asked this question before:

Please review your notes on that topic - thanks!

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Also, I am going to lock this topic down, everything in this thread is a variation of questions asked by @HebaHussein-1981 in previous topics. If there are further issues please review prior posts, and then open a new topic. Thanks!

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