Importing demultiplexed and paired files

User Support
1

Hi all,
I am trying to import two files that are already paired and demultiplexed using the manifest format. I got the following error and I'm wondering if this is a bug:

qiime tools import \

--type 'SampleData[JoinedSequencesWithQuality]' \

--input-path manifest1.csv \

--output-path paired-end-demux.qza \

--input-format PairedEndFastqManifestPhred64

Traceback (most recent call last):

File "/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/tools.py", line 140, in import_data

view_type=input_format)

File "/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 219, in import_data

return cls.from_view(type, view, view_type, provenance_capture)

File "/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 243, in _from_view

recorder=recorder)

File "/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in make_transformation

(self._view_type, other._view_type))

Exception: No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred64'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

An unexpected error has occurred:

No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred64'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

See above for debug info.

I've seen a couple of other problems like this where a new csv file had to be made. Did this, still didn't work. Any ideas? Thank you!

2

Hey there @termofilos!

Did you see this tutorial: Alternative methods of read-joining in QIIME 2 — QIIME 2 2018.8.0 documentation ?

Your --input-format is incorrect - it needs to be a single-end variant, since your reads are pre-joined. Update to --input-format SingleEndFastqManifestPhred64. Also, are you sure your reads are Phred 64? We only see that on very old sequencing product --- virtually everything now is Phred offset 33.

Keep us posted! :qiime2: :t_rex:

3

Thanks for the prompt response! I actually used Phred offset 33 and that fixed it. I'm having another issue now, not sure if i should start a separate topic/thread.

If I'm looking at two joined, already demultiplexed and already split libraries (so i have 2 fastq files, one for each sample) is there any way to compare them on QIIME2? I attained these from a collaborator, so I don't have the files with the barcodes still attached, and can't find a way to compare one fastq file to another. Let me know if i should repost this else where. Thanks!

7

Hi @termofilos,

Yes, I would treat these as SampleData[JoinedSequencesWithQuality] you should be able to use q2-deblur or q2-vsearch with that data. The import process will look the same as for paired end data, you are just changing the --type

If at all possible, you should find that information out, but if it is already demultiplexed as you say, then there probably are no longer barcodes present.