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