importing PrimerSortedDemultiplexed data into qiime2 for windows via ubuntu

[Lau]

Hello all,

I am trying to import data I received into qiime2 for windows wsl ubuntu. Qiime is in the version qiime2-amplicon-2024.2. I have created a manifest file in tsv format in my download folder that looks like this

sample-id	absolute-filepath	direction
sample1	/mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/V3_F357_N_V4_R805-1_TTGTTGCTGT_R1.fastq,/mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/V3_F357_N_V4_R805-1_TTGTTGCTGT_R2.fastq	reverse
sample2	/mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/V3_F357_N_V4_R805-2_GTGTGGTTGT_R1.fastq,/mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/V3_F357_N_V4_R805-2_GTGTGGTTGT_R2.fastq	reverse

my file outpath for my file is"C:\Users\lauri\Downloads\V3_F357_N_V4_R805\soildna1\manifest-file.tsv" however I changed it to read for wsl in /mnt/c format

This is my code to import data

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/manifest-file.tsv
--output-path /mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

However, I keep getting this error

There was a problem importing /mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/manifest-file.tsv:

/mnt/c/Users/lauri/Downloads/V3_F357_N_V4_R805/soildna1/manifest-file.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

'forward-absolute-filepath' is not a column in the metadata. Available columns: 'absolute-filepath', 'direction'

In my tsv file, my column is labled as absolute-filepath. Also I am not sure why it can't identify the data as input-format PairedEndFastqManifestPhred33V2. I have tried Phred64V2 as well

I am new to qiime and working with this type of data in general, so help is appreciated.

[colinbrislawn (Colin J Brislawn)]

Hello Lau,

Welcome to the forums!

@Lau

In my tsv file, my column is labled as absolute-filepath.

Okay good!

@Lau

'forward-absolute-filepath' is not a column in the metadata. Available columns: 'absolute-filepath', 'direction'

Ah, the program want's forward-absolute-filepath but you have absolute-filepath

(The names have to match exactly.)

Once you split up absolute-filepath into forward-absolute-filepath and reverse-absolute-filepath it should work better!

Then we can work on this:

@Lau

Also I am not sure why it can't identify the data as input-format PairedEndFastqManifestPhred33V2. I have tried Phred64V2 as well

Let us know what you try next!