Hi! I am a new user and I am having difficulties importing joined and demultiplexed sequences. I'm running Qiime2 installed with VirtualBox. I've already searched this problem in the Forum before, but I wasn't able to find the solution in my case.
These are the commands I'm trying to use:
qiime tools import
--type 'SampleData[JoinedSequencesWithQuality]'
--input-path merged-manifest-file.tsv
--output-path merged-demux.qza
I've checked the manifest file a several times and it 's correct. It is localed in the same directory as the demultiplexed sequences. But I always get the following error:
Importing 'SingleLanePerSampleSingleEndFastqDirFmt' requires a directory, not merged-manifest-file.tsv
So, I've also tried this:
qiime tools import
--type 'SampleData[JoinedSequencesWithQuality]'
--input-path merged-manifest-file.tsv
--output-path merged-demux.qza
--input-format PairedEndFastqManifestPhred33V2
The last error disappears, but I get a new one:
No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
I'm not sure if the error comes from the input-format because it may be incorrect. I can't find the way to make my commands work.
I have managed to import unjoined demultiplexed sequences before, but I am stuck trying to import the joined sequences in this case. Any advice would be appreciated.
Thank you so much!
