I am trying to import the manifest file into QIIME2, but I get an error as “no such command import-type” and I have verified that I am using 2019 QIIME2. Can you please help with this?
the code is used: qiime tools import
–input path /home/qiime2/desktop/manifest.xlsv
–source format pairedendfastqmanifestphred64
It looks like you may be missing a couple of small but very important details. If you want to type your command on multiple lines, you need to use the
\ character to indicate a line break. Otherwise, the command will be combined together without line breaks. So in your case, your terminal actually interprets your command as
qiime tools import–type ‘sampledata[pairedendseqienceswithquality]’–input path /home/qiime2/desktop/manifest.xlsv–output-path pairend-demux.qza–source format pairedendfastqmanifestphred64
tools plugin does not have an action called
import-type, hence the error
No such command 'import-type'.
For example, notice the difference in behavior between the following two snippets. Copy/paste these into a terminal and observe what happens.
echo "a" "b"
Notice how the behavior differs from this one:
echo "a" \ "b"
Also note that options need to be specified with two dashes,
--, not a single dash,
-, as is the case in the example you shared. If you type in
qiime tools import --help you will see the following:
➜ qiime tools import --help 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]
There you can see exactly what options there are and that they are prepended with
I hope that helps!
Hey! thanks for that, but still i am not able to import, i am using qiime2 in mac. Can you please tell me how to do find the absolute file path? I right clicked the folder in the desktop and in properties i found the path. for instance,
AS1 /home/qiime2/16se1/AS1_combined_R1.fastq.gz forward. This is is format i am using in excel and I import using the command: qiime tools import\
–source-format PairedEndFastqManifestPhred64. I named the excel file as codesmanifest. It gives an error saying the file is not found and my sequences are demultiplexed.
On Mac OS, dragging a file or directory into your terminal will result in pasting the absolute path.