qiime tools import --type EMPPairedEndSequences --input-path /mnt/c/Users/kjharris/Desktop/CFMB2020 --output-path emp-paired-end-sequences.qza
There was a problem importing /mnt/c/Users/kjharris/Desktop/CFMB2020:
Missing one or more files for EMPPairedEndDirFmt: ‘forward.fastq.gz’
All three fastq.gz files are alone in the desktop folder:
On a previous attempt Q2 provided the following: qiime tools import \
Imported /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences as EMPPairedEndDirFmt to emp-paired-end-sequences.qza
Any thoughts on what I am doing wrong to run this initial script? I ran the q2 updates earlier today so I have updated to 2020.8 Thank you for any help!
I am wondering if I need to place the three fastq.gz files in a zipped folder?
I think that I had to create a zipped file before when I imported, but the zipped file does not seem to be recognized. I am using ubuntu
(qiime2-2020.8) [email protected]:~ /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped
-bash: /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped: No such file or directory
(qiime2-2020.8) [email protected]:~ /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/
-bash: /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/: Is a directory
(qiime2-2020.8) [email protected]:~ C:\Users\kjharris\Desktop\CFMB2020\EMPPairedEndSequences\Zipped.zip
C:UserskjharrisDesktopCFMB2020EMPPairedEndSequencesZipped.zip: command not found
(qiime2-2020.8) [email protected]:~ /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped.zip
-bash: /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped.zip: Cannot allocate memory
I updated my Mac to q2 2020.8 and I have the forward, reverse, and barcodes in a zip file on my desktop now, but I am still having trouble making the initial emp-paired-end-sequences.qza
(qiime2-2020.8) Kyles-MBP:CFMB2020 kyleharris$ qiime tools import \ --type EMPPairedEndSequences \ --input-path /Users/kyleharris/Desktop/CFMB2020/Archive.zip \ --output-path /Users/kyleharris/Desktop/CFMB2020 emp-paired-end-sequences.qza
Usage: qiime tools import [OPTIONS]
Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/
for usage examples and details on the file types and associated semantic
types that can be imported.
–type TEXT The semantic type of the artifact that will be
created upon importing. Use --show-importable-types
to see what importable semantic types are available
in the current deployment. [required]
–input-path PATH Path to file or directory that should be imported.
–output-path ARTIFACT Path where output artifact should be written.
–input-format TEXT The format of the data to be imported. If not
provided, data must be in the format expected by the
semantic type provided via --type.
–show-importable-types Show the semantic types that can be supplied to
–type to import data into an artifact.
Show formats that can be supplied to --input-format
to import data into an artifact.
–help Show this message and exit.
There were some problems with the command:
(1/4) Missing option ‘–type’.
(2/4) Missing option ‘–input-path’.
(3/4) Missing option ‘–output-path’.
(4/4) Got unexpected extra arguments ( --type EMPPairedEndSequences --input-
path /Users/kyleharris/Desktop/CFMB2020/Archive.zip --output-path
(qiime2-2020.8) Kyles-MBP:CFMB2020 kyleharris$
(qiime2-2020.8) Kyles-MBP:~ kyleharris$ qiime tools import --type EMPPairedEndSequences --input-path /Users/kyleharris/Desktop/CFMB2020/rawsequencing --output-path /Users/kyleharris/Desktop/CFMB2020/emp-paired-end-sequences.qza
Imported /Users/kyleharris/Desktop/CFMB2020/rawsequencing as EMPPairedEndDirFmt to /Users/kyleharris/Desktop/CFMB2020/emp-paired-end-sequences.qza
Got it to work!
Glad you sorted things out @mudbugecology!
Just for posterity (to clarify for other users reading this topic), it looks like the issue is that you were pointing at the wrong directory:
But your files were not in
/mnt/c/Users/kjharris/Desktop/CFMB2020, they were in
Looks like you moved these all into a separate directory and got this to work:
Thanks for sticking with it, and also for reporting back that you solved it!
Thanks, Nicholas! Glad to be back with another sample and running Q2. Have a wonderful Thanksgiving. Kyle
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