Hi everyone,
I am new to Qiime2 (version -2019.4, conda) and I am having some trouble importing my data. The sequencing facility provided me with demultiplexed merged data (30 samples = 30 files containing merged reads) in fastq.gz format.
I created a manifest.csv with header "sample-id,absolute-filepath,direction" and used the following command:
*qiime tools import *
*--type 'SampleData[JoinedSequencesWithQuality]' *
*--input-path $Absolute-path/manifest_merged4.csv *
*--output-path $Absolutepath/joined-demux.qza *
--input-format SingleEndFastqManifestPhred33
The error I get after running the command is
Regarding the manifest: I checked my manifest file multiple times (e.g. separation by tab, no excessive tabs, filepath within manifest, filenames etc.etc.) and tried to change format of the manifest and files respectively to ".tsv"/".txt" and "fastq". I also tried to change --input-format from "...Phred33" to "...Phred33V2" and then using tabs instead of coma's as separation and removing "direction" from the header. In this case I got this particular error:
Regarding the command, I also tried to change --type from "JoinedSequencesWithQuality" to "SequencesWithQuality", but nothing changed.
I already saw the tutorials about importing manifests and also looked on the Forum for similar questions. Especially the Forum really helped me (the error mentioned above is just the latest one I got).
I would really appreciate some help here. I am definitively missing something here 
Hereby the two manifests I use:
manifest_merged4.csv (4.3 KB)
manifest_merged3.txt (4.0 KB)
Cheers,
Nicholas
forum.
