Moving Pictures tutorial error

[flyinleonard (Jared)]

In terminal, I keep getting an error as I try to work through the tutorial. I'm not sure what I am supposed to do.

(qiime2-2017.12) Jareds-MacBook-Air-2:desktop jared$ qiime tools import
Usage: qiime tools import [OPTIONS]

Error: Missing option "--type".
(qiime2-2017.12) Jareds-MacBook-Air-2:desktop jared$ qiime tools import \

type EMPSingleEndSequences
Usage: qiime tools import [OPTIONS]

Error: Missing option "--type".
(qiime2-2017.12) Jareds-MacBook-Air-2:desktop jared$ --type empsingleendsequenes \

--input-path emp-single-end-sequences
--output-path emp-single-end-sequences.qza
-bash: --type: command not found
(qiime2-2017.12) Jareds-MacBook-Air-2:desktop jared$ qiime demux emp-single
--i-seqs emp-single-end-sequences.qza
--m-barcodes-file sample-metadata.tsv
--m-barcodes-category barcodesequence
--o-per-sample-sequences demux.qza
Usage: qiime demux emp-single [OPTIONS]

Error: Invalid value for "--i-seqs": Path "emp-single-end-sequences.qza" does not exist.
(qiime2-2017.12) Jareds-MacBook-Air-2:desktop jared$

I'm not sure where to go from heree.

[thermokarst]

Hi @flyinleonard, sorry to hear things aren’t going well. It looks like you aren’t copying out the commands listed on the tutorial in full. For example, your second command listed there is:

$ qiime tools import \
  --type EMPSingleEndSequences

but, if you check the Moving Pictures Tutorial, the command listed is actually:

$ qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza

It is very important to ensure that the commands you write (or copy) are complete, and contain all of the elements relevant to that particular command. In the case I outline here, you were providing an incomplete command, because it was missing the --input-path and --output-path flags. Hope that helps get you moving on the right track. If not, you know where to find us! Thanks

[flyinleonard (Jared)]

I have tried entering and reentering the information. I have entered it exactly as it appears on the tutorial. I have copy and pasted it exactly and it is still saying there is an error.

(qiime2-2017.12) Jareds-MacBook-Air-2:~ jared$ qiime tools import \

--type EMPSingleEndSequences
--input-path emp-single-end-sequences
--output-path emp-single-end-sequences.qza
Usage: qiime tools import [OPTIONS]

Error: Invalid value for "--input-path": Path "emp-single-end-sequences" does not exist.

[flyinleonard (Jared)]

When I keep going I get a similar error.

(qiime2-2017.12) Jareds-MacBook-Air-2:~ jaredleonard$ qiime demux emp-single \

--i-seqs emp-single-end-sequences.qza
--m-barcodes-file sample-metadata.tsv
--m-barcodes-category BarcodeSequence
--o-per-sample-sequences demux.qza
Usage: qiime demux emp-single [OPTIONS]

Error: Invalid value for "--i-seqs": Path "emp-single-end-sequences.qza" does not exist.
(qiime2-2017.12) Jareds-MacBook-Air-2:~ jaredleonard$

Thank you for helping.

[thermokarst]

Hi @flyinleonard --- not only do you need to make sure you copy the individual commands in full (and correctly), you also need to ensure that you run all of the provided commands, in the order that they are listed.

@flyinleonard

Error: Invalid value for “–input-path”: Path “emp-single-end-sequences” does not exist.

This error suggests you didn't successfully complete the initial steps in the tutorial related to making the import data directory, and possibly related to downloading the tutorial data.

In general, if you miss any step, the subsequent downstream steps are going to break down for you. I would suggest that you restart at the beginning of the tutorial - take your time and enjoy yourself ! Keep us posted!