I am a very beginner user of Qiime2 and I am new at the programing language at all. I am trying to learn Qiime2.
I am now following the “Moving pictures tutorial”. All goods till the step “Obtaining and importing data”.
When I type the following command
qiime tools import
the terminal says "no such command “import --type” but when I type the same command without “–type” it says missing options “–type”
Maybe this seems a basic question for the most of you, but did someone face this issue before?
Could you please tell me where do I make a mistake?
just in case, can you please suggest me any other equipment to learn programing language?
Thank you for your attention and your help!
Hi @chiara! Thanks so much for writing, and sorry to hear you are having some difficulties. It looks like you ran the following command:
qiime tools import
but what is missing is the
\ (backslash) character to tell your shell that you are splitting one command over multiple lines (this is how most/all of the command examples in the docs are formatted). Generally speaking, when you run a command (any command, not just QIIME 2) on the command line, you run one command per line. The backslash is used to indicate when a command is spread out over multiple lines:
qiime tools import \
--type EMPSingleEndSequences \
--input-path emp-single-end-sequences \
(note the trailing slashes at the ends of the lines, this tells your shell to join the lines together when running the command)
Alternatively, you could format it in one line:
qiime tools import --type EMPSingleEndSequences --input-path emp-single-end-sequences --output-path emp-single-end-sequences.qza
It really just comes down to personal preference. We split commands across multiple lines for readability, but again, this is a bit subjective!
I would like to mention, none of this is specific to QIIME 2, but rather has to do with general command-line computing. If you are interested in some command line computing resources, please check out this list on readiab.org.
Please don’t hesitate to reach out if you get stuck or have any questions!
I am still facing some issue with the import tool and following the related tutorial seems to be not helpful for me.
I need to convert my fastq file in artifact (.qza).
I am running the command below:
qiime2 tools import \ --type Fasta-qual-mapping-files [sequences] \ --import-path name of my file \ --output name of the file.qza
the terminal keeps saying Missing option "–type"
I think I don’t understand exactly what information should I type after “–type”.
Do you have any ideas about it?
Thanks for your attention!
Have you had a chance to review the Importing tutorial? There are a few ways to import your fastq files, but the best option depends on how they are arranged, formatted, and named. If you followed the EMP protocol, I would suggest starting there; if your files are in Casava 1.8 format, start here; and if they aren’t in either of those arrangements, then check out the fastq manifest formats. There are lots of
importing examples here on the forum, and many of them are specifically about the
fastq-manifest formats — please take a look through and see what makes the most sense for you and your data! Let us know if you get stuck or have any questions.
Please see my comment above about the importing tutorial — the command you have written out here isn’t a valid import command, but I provided several links to examples above!
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