I have demultiplexed paired end reads in the following format:
israa_s1_S1_L001_R1_001.fastq.gz
israa_s1_S1_L001_R2_001.fastq.gz
To match the casave 1.8 format, I changed the file names as:
israas1_L001_R1_001.fastq.gz
israas1_L001_R2_001.fastq.gz
I have uploaded them in the collection tab and built them as a List collection and named it:“Collection1”
Then, I went to the qiime2 import tool and selected the following:
- Type of data to import: SampleData[PairedEndSequencesWithQuality]
- Qiime2 file format to import from: Casava One Eight Single Lane Per Sample Directory Format
- Select a mechanism: Use collection to import
- Elements: Collection1
When I run the tool, it gives me an error with the following note:
qiime2.core.exceptions.ValidationError: Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’
What files could be missing, appreciate any help. Thank you in advance.
1 Like
Welcome @Israa_Cheikh !
We have examples in this topic section → Unable to import my files as .qza - #2 by jennaj
. Be sure to see the link to the example Galaxy history and the Qiime2 tutorial.
Since you have single end data, not paired end, you will be using a simple list collection shape (the Galaxy folder type) and the option on the Qiime2 Import form for a (single end Qiime2 artifact type). The expected format of the @ lines will be on the form.
From where you are now, you can try two different things to get this working.
- Method 1
Recreate the collection and use the toggle to NOT remove the extensions from the element identifiers. Keep the full original file names. You can extract the element identifiers to check.
- Method 2
This is for situations when the file extensions were removed during collection creation.
Toggle the option on the Qiime2 Import tool form Append an extension?
This didn’t work for your data since one of the internal sections was missing in the element identifiers (from other manipulations), but you might want to use this method later. The collection builder functions will strip off the extensions by default, so using this option is pretty common.
I put examples of both back into your shared history. Please feel free to get a copy to review the details of why this works. Let me know once you have done that and I’ll delete my copy. 
Screenshot of history with element datasets expanded, tagged
1 Like
