Qiime2 import error: Errno2

[dylanv (Dylan Vecchione)]

Hello,

I am experiencing a strange error that for some reason includes a reference to a missing Microsoft Outlook sdk file every time I try to import my raw demultiplexed PE fastq files:

(qiime2) dvecchione@Dylans-MBP-9 F2 % qiime tools import \      
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path / \                                 
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path F2.qza
              
Traceback (most recent call last):
  File "/Users/dvecchione/miniforge3/envs/qiime2/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 266, in import_data
    artifact = qiime2.sdk.Artifact.import_data(type, input_path,
  File "/Users/dvecchione/miniforge3/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 320, in import_data
    md5sums = util.md5sum_directory(path)
  File "/Users/dvecchione/miniforge3/envs/qiime2/lib/python3.8/site-packages/qiime2/core/util.py", line 135, in md5sum_directory
    sums[os.path.relpath(path, start=directory)] = md5sum(path)
  File "/Users/dvecchione/miniforge3/envs/qiime2/lib/python3.8/site-packages/qiime2/core/util.py", line 119, in md5sum
    with open(str(filepath), mode='rb') as fh:

FileNotFoundError: [Errno 2] No such file or directory: '/Applications/Microsoft Outlook.app/Contents/Frameworks/AppNexusNativeMacOSSDK.framework/PrivateHeaders'

An unexpected error has occurred:

  [Errno 2] No such file or directory: '/Applications/Microsoft Outlook.app/Contents/Frameworks/AppNexusNativeMacOSSDK.framework/PrivateHeaders'

See above for debug info.

I am running q2cli 2023.07.0 conda install. I am on macOS 14.0 M2 running conda 23.3.1 through an apple silicon install of minforge3 with a qiime2 env with python 3.8.17. I tried re-running the import command with a --verbose flag but it errored saying that was not an option. Thank you for your help.

[Oddant1]

Hello @dylanv. It looks like you gave your root directory / as your input path which means you are basically trying to import everything on your computer into a QIIME 2 artifact. If you meant to import the directory you were in at the time then you would want to give . as your input directory.

Some quick terminal tips, / is the root of your filesystem (basically everything on your computer is somewhere under root), ~ is your home directory, .. is the parent of the directory you are currently in, and . is the directory you are currently in.

[dylanv (Dylan Vecchione)]

Hello @Oddant1 ,

It's always the most simple fix that I look past. Thank you very much for your help and tips!