importing files to qiime2

[ji1691 (jerald)]

Hi everyone,

I've been having issues with importing files

I used the following to import my files

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path raw --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza

It gives me the following error

There was a problem importing raw/:

Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

Here is a screenshot of the filenames I have

It has worked before when I was using another dataset and on a different server.
I wonder what could be the issue.

Thank you!

[Oddant1 (Anthony Simard)]

Hello @ji1691,

This error

Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

Is saying each of your filenames must match the pattern

'.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

It looks like your filenames are missing the L[0-9][0-9][0-9] portion of the filename that is a part of the CasavaOneEight spec. You need to add that portion to the correct part of each of your file names e.g.

EV_M_0_Jun23_A_S108_L001_R1_001.fastq.gz

Alternatively, you can use a manifest format to import by creating a manifest file that maps each sample name to the filepath(s) for the sample

https://docs.qiime2.org/2024.10/tutorials/importing/#fastq-manifest-formats

[ji1691 (jerald)]

Hi @Oddant1,

Thank you!

Changing the name worked perfectly!

If I use the manifest file, is this a better way to not change the sample names?

[Oddant1 (Anthony Simard)]

The manifest file or changing the file names will both get you the same results in QIIME 2, it's just up to you which process you find easier.

[ji1691 (jerald)]

Thank you so much for your help!