Importing demultiplexed and paired files

[termofilos]

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!

[thermokarst]

Hey there @termofilos!

@termofilos

I am trying to import two files that are already paired and demultiplexed using the manifest format

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:

[termofilos]

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!

[ebolyen (Evan Bolyen)]

Hi @termofilos,

@termofilos

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?

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

@termofilos

I attained these from a collaborator, so I don’t have the files with the barcodes still attached,

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.