Trouble importing paired end data: No transformation error

[mmelendrez (Mel Melendrez)]

I am getting an error importing demultiplexed paired end Illumina data. I saw the October 2017 (Trouble importing demultiplexed PE data) post but my command still doesn’t work even with a properly formatted manifest:

Command:
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path Efalcata_manifest.csv --output-path Efalcata_pe_demux.qza --source-format PairedEndFastqManifestPhred33

Error:
Traceback (most recent call last):
File “/Users/mel_local/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/tools.py”, line 112, in import_data
view_type=source_format)
File “/Users/mel_local/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 211, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/Users/mel_local/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 235, in _from_view
recorder=recorder)
File “/Users/mel_local/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/core/transform.py”, line 53, in make_transformation
(self._view_type, other._view_type))
Exception: No transformation from <class ‘q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33’> to <class ‘q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt’>

An unexpected error has occurred:

  No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

See above for debug info.

I have checked my manifest file and it looks fine - CSV formatted:
sample-id,absolute-filepath,direction
pop1,/Users/mel_local/Analysis/FalcataProject/pop1/pop1_RTF_R1.fastq,forward
pop1,/Users/mel_local/Analysis/FalcataProject/pop1/pop1_RTF_R2.fastq,reverse
pop2,/Users/mel_local/Analysis/FalcataProject/pop2/pop2_RBF_R1.fastq,forward
pop2,/Users/mel_local/Analysis/FalcataProject/pop2/pop2_RBF_R2.fastq,reverse
pop3,/Users/mel_local/Analysis/FalcataProject/pop3/pop3_LTF_R1.fastq,forward
pop3,/Users/mel_local/Analysis/FalcataProject/pop3/pop3_LTF_R2.fastq,reverse
pop4,/Users/mel_local/Analysis/FalcataProject/pop4/pop4_LBF_R1.fastq,forward
pop4,/Users/mel_local/Analysis/FalcataProject/pop4/pop4_LBF_R2.fastq,reverse

Any advice would be appreciated.

[thermokarst (Matthew Ryan Dillon)]

Hi @mmelendrez, you are so close! You just need to update the type to indicate that you are importing paired end sequences with quality:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path Efalcata_manifest.csv \
  --output-path Efalcata_pe_demux.qza \
  --source-format PairedEndFastqManifestPhred33

Give that a shot and let us know how it goes!

[mmelendrez (Mel Melendrez)]

I knew it had to be something simple! It looks like it’s running now. And thank you for being kind with fielding simpler syntax issues.

[mmelendrez (Mel Melendrez)]

It worked! Many thanks!