“There was a problem with importing oral_seq/oral_casava_import/:
Unrecognized file (oral_seq/oral_casava_import/.git/hooks/post-update.sample) for CasavaOneEightSingleLanePerSampleDirFmt.”
Hi @Lotte, @jwdebelius is correct, the manifest format is easier to work with... your files can be named anything and stored in all different places. So you could have saved yourself the trouble of renaming your files!
That said, I just want to address this problem:
The casava1.8 import format expects that only casava 1.8 fastq.gz files will be present in the input directory path (oral_seq/oral_casava_import/). Nothing else should be there. You have a hidden directory (.git) in there that contains at least one file (.git/hooks/post-update.sample), so QIIME 2 is getting upset! Either remove that directory and all other non-fastq.gz filepaths from your input directory path, or use the manifest format.