Error to import data with command line "qiime tools import"

Hello,

I have a problem with the command line « qiime tools import ». I tried to do as mentioned in the tutorial (Importing data) with the files L2S357_15_L001_R1_001.fastq.gz and L2S357_15_L001_R2_001.fastq.gz.
(ex : JF1AR1_TAGTAC_L001_R1_001.fastq.gz)

Please find below an example of my personal demultiplexed files JF1AR1_TAGTAC_L001_R1_001.fastq.gz :

[email protected]:39:000000000-APEBN:1:2107:15115:1526 1:N:0:TAGTAC_
_GTGCCAGCCGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCTGGCGGTTCTGTTTTTCTGATGTTATTTCCCAGGTCTCACCCTTTTAACTGCATTCTTATCTTCCTTTCTATATTATGTCTCTCGTTGGTAGAATTCCCCTTTTATCAGTTAAATTCTTAGATATTCTTTTTTTTTCCGATTGCTTATTCTGCCCCCTGTGATAATACTTTCTCTCATGCTC_
_+_
_<[email protected][email protected][email protected],EE8;-C;@AA,C-CF7<EE8-,,:C-CE9,,C+8+,,,,+8,6+++++6++8>8,,,,,,+,,,,<,<,,,,<9<5,,+,:B?,,99:A,,,,<B,:,<<[email protected],,:<,8<,,,,8,,,,<,<,<5,,,,+++,,8,,,,<>33,3,:,:,,<,,:,,,,8,7,@,,,@,@,3,,,,,**5*33**8**2,,,,,,,,2,*14<*+++2+,5+25++2++?>,?+,++_

etc…

I tried:

(qiime2-2017.2) [email protected]:~/qiime2/qiime2-moving-pictures$ qiime tools import \
--type SampleData[PairedEndSequencesWithQuality] \
--input-path R1R2 (my name of folder) \
--source-format SingleLanePerSamplePairedDirFmt \
--output-path demux-paired-end-Toul.qza

I got the error message: TypeError: No format: SingleLanePerSamplePairedDirFmt
(Complete error message is given below)

I tried several things without any success. Your help would by greatly appreciated.
Thank you.

Ylana.

Traceback (most recent call last):
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/util.py", line 91, in parse_format
    format_record = pm.formats[format_str]
KeyError: 'SingleLanePerSamplePairedDirFmt'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/q2cli-2017.2.0-py3.5.egg/q2cli/tools.py", line 62, in import_data
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/result.py", line 158, in import_data
    view_type = qiime2.sdk.parse_format(view_type)
  File "/home/cidam/miniconda2/envs/qiime2-2017.2/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/util.py", line 93, in parse_format
    raise TypeError("No format: %s" % format_str)
TypeError: No format: SingleLanePerSamplePairedDirFmt

Hi @ylana_sauvaget! The source format SingleLanePerSamplePairedDirFmt doesn’t exist in QIIME 2 version 2017.2. You’ll need to use CasavaOneEightSingleLanePerSampleDirFmt as your source format. Here’s the relevant section of the importing tutorial with an example.

If you’re running an older version of QIIME 2 (e.g. version 2.0.6), we highly recommend upgrading to the latest version (2017.2) as we only support the latest version of QIIME 2 while in alpha development.

1 Like

Thank you, very much for your help ! I changed my format and it works.

ylana

2 Likes

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