I have what I am pretty sure are casava paired end files that are named as such:
When I try to import using:
qiime tools import \
I get the error:
There was a problem importing fastq:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R_001\\.fastq\\.gz'
I am pretty sure the files are missing the barcode identifiers and am wondering if there is a workaround or do I need to contact the authors in getting the barcode identifiers (its from a public database).
Any help would be appreciated!
This is because that format has a specific naming schema, as outlined
@sleva88, welcome to !
I think the names of your files, e.g. C1_S43_L001_R1_001_trimmed.fastq end up violating the naming schema for Casava. I think if you remove _trimmed from the file names it should work.
Alternatively, you can leave the files named as they are and try the Manifest format.
Thanks for the link to the related question. I will try the manifest format and see how that goes.
Also this might be the tiniest of details but the example manifest file in the qiime tutorial reads as such:
And I am not sure if sample.1 is written with the period intended or if that is a mistake. Just wanted to make you guys aware just in case it is a mistake
@Sam_Degregori, this is just to highlight the acceptable
sample-id formats. You can check out the
Recommendations for Identifiers documentation for more details.
June 13, 2021, 4:07am
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