importing fastq.gz to output emp-paired-end-sequences.qza

Technical Support
1

Running:
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:
barcodes.fastq.gz
forward.fastq.gz
reverse.fastq.gz

On a previous attempt Q2 provided the following: qiime tools import \

--type EMPPairedEndSequences
--input-path /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences
--output-path emp-paired-end-sequences.qza
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!

2

I am wondering if I need to place the three fastq.gz files in a zipped folder?

3

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) kjharris@6SS4NV2:~ /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) kjharris@6SS4NV2:~ /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/
-bash: /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/: Is a directory
(qiime2-2020.8) kjharris@6SS4NV2:~ C:\Users\kjharris\Desktop\CFMB2020\EMPPairedEndSequences\Zipped.zip C:UserskjharrisDesktopCFMB2020EMPPairedEndSequencesZipped.zip: command not found (qiime2-2020.8) kjharris@6SS4NV2:~ /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped.zip
-bash: /mnt/c/Users/kjharris/Desktop/CFMB2020/EMPPairedEndSequences/Zipped.zip: Cannot allocate memory

4

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.

Options:
–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.
[required]
–output-path ARTIFACT Path where output artifact should be written.
[required]
–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-importable-formats
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
/Users/kyleharris/Desktop/CFMB2020 emp-paired-end-sequences.qza)
(qiime2-2020.8) Kyles-MBP:CFMB2020 kyleharris$

5

(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!

1 Like
6

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 /mnt/c/Users/kjharris/Desktop/:

Looks like you moved these all into a separate directory and got this to work:

:partying_face:

Thanks for sticking with it, and also for reporting back that you solved it!

7

Thanks, Nicholas! Glad to be back with another sample and running Q2. Have a wonderful Thanksgiving. Kyle

2 Likes
8

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