Error in importing demultiplexing data

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1

Hi everyone,
I am trying to do the microbiome analysis of the following dataset ERR2518120.fastq.gz ERR2518121.fastq.gz ERR2518122.fastq.gz ERR2518123.fastq.gz ERR2518124.fastq.gz.

I am following this command-

[mkarim1@compute-3-24 microbiome]$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /project/meisel/mkarim2/microbiome --input-format CasavaOneEightLanelessPerSampleDirFmt --output-path demux-single-end.qza

But I find the following error-

There was a problem importing /project/mesel/mkarim1/microbiome:
Missing one or more files for CasavaOneEightLanelessPerSampleDirFmt: '.+_.+_R[12]_001\.fastq\.gz'

What might be the cause and possible solution?
Thanks

2

Hello @MdEkramulKarim1,

Welcome to the forums! :qiime2:

This is a very specific format that only imports files with names like this:
L2S357_15_L001_R1_001.fastq.gz

Because your file names are different, you may have better luck using the Fastq manifest format, which is way more flexible. If these files are all forward reads, one of the SingleEndFastqManifest- formats should work well.

Let us know if you have any questions!

3

Thank you, But I tried with the following command with menifest file

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /project/meisel/mkarim2/microbiome2 --input-format SingleEndFastqMenifestPhred33V2 --output-path demux-single-end.qza

And it is giving me the following error
demux-single-end.qza
Traceback (most recent call last):
File "/project/meisel/apps/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/util.py", line 90, in parse_format
format_record = pm.formats[format_str]
KeyError: 'SingleEndFastqMenifestPhred33V2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/project/meisel/apps/qiime2-2022.11/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/project/meisel/apps/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 287, in import_data
view_type = qiime2.sdk.parse_format(view_type)
File "/project/meisel/apps/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/util.py", line 92, in parse_format
raise TypeError("No format: %s" % format_str)
TypeError: No format: SingleEndFastqMenifestPhred33V2

An unexpected error has occurred:

No format: SingleEndFastqMenifestPhred33V2

See above for debug info.

Menifest_file.txt (168 Bytes)
sample_metadata2.txt (6.3 KB)
My sample_metadata and menifest_files are attached herewith. Thanks in advance

4

Hello,

It's "Manifest" nit "Menifest". Please, pay attention.

5

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