Denoising paired ends with DADA2 Error

Hi
i am working with illunina miseq spaired end equences (301nt) when i running dada2 denoise-paired (qiime2-2019.7 conda enviroment)

(qiime2-2019.7) [email protected]:~/Projects/CU/Qiime2$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trunc-len-f 280–p-trunc-len-r 260 --p-n-threads 20 --o-table output_data/table.qza --o-representative-sequences output_data/rep-seqs.qza --o-denoising-stats output_data/denoising-stats.qza

i received this error:

Traceback (most recent call last):
File “/home/pufo/miniconda2/envs/qiime2-2019.7/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1135, in invoke
sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 641, in make_context
self.parse_args(ctx, args)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/command.py”, line 60, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1469, in handle_parse_result
value = self.full_process_value(ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/option.py”, line 149, in full_process_value
return super().full_process_value(ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1790, in full_process_value
return Parameter.full_process_value(self, ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1438, in full_process_value
value = self.process_value(ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1428, in process_value
return self.type_cast_value(ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/option.py”, line 203, in type_cast_value
return super().type_cast_value(ctx, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1417, in type_cast_value
return _convert(value, (self.nargs != 1) + bool(self.multiple))
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1415, in _convert
return self.type(value, self, ctx)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/types.py”, line 39, in call
return self.convert(value, param, ctx)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/type.py”, line 83, in convert
return self._convert_primitive(value, param, ctx)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/click/type.py”, line 195, in _convert_primitive
return qiime2.sdk.util.parse_primitive(self.type_expr, value)
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/core/type/util.py”, line 218, in parse_primitive
result.append(_interrogate_types(allowed, v))
File “/home/pufo/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/core/type/util.py”, line 175, in _interrogate_types
raise _COERCE_ERROR
ValueError: Could not coerce value based on expression provided.

Thanks!

Welcome to the forum @pufetin!

This is a bit of a cryptic error message, essentially saying that you are inputting a value that QIIME 2 cannot understand. To be more specific, it is expecting an integer value for the --p-trunc-len-f parameter but you accidentally lost a space, so instead this is written:

add a space after the 280 and QIIME 2 will be much happier!

Good luck!