Importing the demultiplexed merged data

[thermokarst]

@adoloman

This all completely does NOT make sense.

Ah, sorry to hear that! Is there something specific that doesn't make sense here?

@adoloman

First of all, the manual on importing the files does not specify that everything should be located in the same directory;

I think there might be a misunderstanding here --- no such requirement exists here! This actually ties into my post above --- the import process depends on you telling QIIME 2 where to find files. This happens in two place. First, you tell QIIME 2 where your manifest file is (--input-path), then, inside the manifest file you tell QIIME 2 where to find the individual files necessary for import (there are the entries under the column absolute-filepath). Again, you have to be explicit here, and this really is just the nature of computing (that is, it isn't a problem specific to or unique to QIIME 2).

@adoloman

Secondly, I DID specify the CORRECT path where both the manifest file and the fastq files were located, in the command for qiime execution in the Terminal. An error was constantly thrown out, until I cd-ed into the directory where fastq files and manifest file was located.

I took a quick read through your commands above:

@adoloman

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path for-qiime2
–source-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

you are specifying the wrong source format for working with a manfiest file --- this should be --source-format PairedEndFastqManifestPhred33, CasavaOneEightSingleLanePerSampleDirFmt is an entirely different format.

@adoloman

This is VERY illogical and thus, should be specified on the manual webpage.

It sounds like you maybe haven't had a chance to review the Importing data tutorial yet - I highly recommend it.

Hope that helps!