Error importing taxonomy file (zsh: no matches found: FeatureData[Taxonomy]

Technical Support
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1

Hello - I am running into an error trying to import a taxonomy file. This issue is related to a previous one that is closed here:

However, I have tried the solution offered there and continue to run into the error. I have tried the code below in these miniconda Mac M2 versions of QIIME 2: 2020.6, 2022.11, amplicon-2023.9, and receive the same error. I have also tried re-typing the code.

qiime tools import \
  --input-path /home/jpshaffer/allergy_microbes/data/global_soil_mycobiome/global_soil_myco_metadata_features_taxonomy.txt \
  --input-format TSVTaxonomyFormat \
  --output-path /home/jpshaffer/allergy_microbes/data/global_soil_mycobiome/global_soil_myco_metadata_features_taxonomy.qza \
  --type FeatureData[Taxonomy] \
  --verbose

I'm not sure what the source of the error is and worry it's something specific to my system.
Thanks in advance for any insight.
Justin

2

@Lichen can you DM me the file you're trying to import please?

4

@Lichen I am able to import it on my system in both 2023.9 and 2024.2. One thing worth noting is that qiime tools import does not have a verbose flag, and in the sample command you pasted there you pass in a --verbose flag. Have you tried importing it without that flag?

5

Thanks for your reply. Yes, I have tried running the command without the verbose flag and get the same error. I added the flag as recommended by the forum posting policies, but it's good to know it doesn't work for this.

OK so it does seem like it is system specific. I will try to import it on another machine later, however is there anything we can do to try and troubleshoot the issue further on this machine?

Thanks in advance,

Justin

6

I talked to a coworker who is on Mac (I'm on Linux) and he identified the issue. You are in zsh and as such need to escape the opening and closing square brackets in FeatureData[Taxonomy] like so:

qiime tools import \
  --input-path /home/jpshaffer/allergy_microbes/data/global_soil_mycobiome/global_soil_myco_metadata_features_taxonomy.txt \
  --input-format TSVTaxonomyFormat \
  --output-path /home/jpshaffer/allergy_microbes/data/global_soil_mycobiome/global_soil_myco_metadata_features_taxonomy.qza \
  --type FeatureData\[Taxonomy\] \
7

Basically, zsh interprets those as some kind of special character, putting a \ in front of them tells zsh you are just using those characters as themselves not for whatever special meaning zsh gives them.

1 Like
8

Thank you so much for identifying this issue! I sincerely appreciate it. I was going crazy trying to figure out why it wasn't accepting that as a type.

9

Just a quick reply to note that surrounding the type with quotes also seemed to work:

qiime tools import \
  --input-path /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_metadata_features_taxonomy.txt \
  --input-format TSVTaxonomyFormat \
  --output-path /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_metadata_features_taxonomy.qza \
  --type 'FeatureData[Taxonomy]'

Thanks again for helping to resolve this!

3 Likes