With the addition of
QIIME1DemuxFormat as a source-format, Qiime2 can now import Qiime1-demultiplexed fasta files (i.e.
split_libraries_fastq.py). However, this does not seem to work for the equivalent fastq files (i.e.
To illustrate, this works when the input is a FASTA file (no quality scores),
qiime tools import \ --type SampleData[Sequences] \ --input-path seqs.fna \ --output-path demux.qza \ --source-format QIIME1DemuxFormat
but not when the input is a FASTQ file (with quality scores),
qiime tools import \ --type SampleData[SequencesWithQuality] \ --input-path seqs.fastq \ --output-path demux.qza \ --source-format QIIME1DemuxFormat
for which it yields the following error
An unexpected error has occured: No transformation from <class 'q2_types.per_sample_sequences._format.QIIME1DemuxFormat'> to <class ' q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFast qDirFmt'> See above for debug info.
Is my import command correct? If yes, is the error due to the lack of a transformation that enables sourcing a
SampleData[SequencesWithQuality]? Would it be possible to code such a transformation in upcoming releases?
There are two related discussions regarding this issue.
- One user suggested the manifest file approach for importing data. However, this assumes that the library of sequences is demultiplexed into multiple files, one for each sample. This is not always the case for files previously demultiplexed in Qiime1 where usually a single file contains all demultiplexed samples.
- Another user has created a clever way to circumvent this problem but this somewhat unnecessarily requires splitting the files via Qiime1 and creating a manifest file.
Thanks again for your work on on Qiime! It has been really nice to witness your progress in the newest release.