Hello,
I am very new to Qiime2 and trying to create my QIIME 2 artifact. I am trying to follow the Casava 1.8 paired-end demultiplexed fastq example but the "--source-format" column is confusing me. I am trying to run this command:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path liver_ --source-format LiverDir --output-path liver-demux-paired-end.qza
An example of how my data is named is: TL9e_1.fq.gz TL9e_2.fq.gz, denoting sampleID_foward/reverse.fq.gz
I am getting the error "TypeError: No format: LiverDir" (full error message below). Any help of advice would be appreciated, Thanks!
Traceback (most recent call last):
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/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: 'LiverDir'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/bin/qiime", line 6, in
sys.exit(q2cli.main.qiime())
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli-2017.2.0-py3.5.egg/q2cli/tools.py", line 62, in import_data
File "/s/angus/index/common/tools/miniconda3/envs/qiime2/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 "/s/angus/index/common/tools/miniconda3/envs/qiime2/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: LiverDir
(qiime2) weinroth@angus:/s/angus/index/projs/mega_tylan/analysis/XIT/livers$