diversity core-metrics-phylogenetic error

I am using qiime2.2019.04 version and I am getting error while doing core phylogenetic analysis, please advise if I am doing anything wrong?

$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 36000–m-metadata-file metadata.txt --output-dir core-metrics-results

Traceback (most recent call last):
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/bin/qiime”, line 11, in
sys.exit(qiime())
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1135, in invoke
sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 641, in make_context
self.parse_args(ctx, args)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/click/command.py”, line 59, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1469, in handle_parse_result
value = self.full_process_value(ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/click/option.py”, line 149, in full_process_value
return super().full_process_value(ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1790, in full_process_value
return Parameter.full_process_value(self, ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1438, in full_process_value
value = self.process_value(ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1428, in process_value
return self.type_cast_value(ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/click/option.py”, line 203, in type_cast_value
return super().type_cast_value(ctx, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1417, in type_cast_value
return _convert(value, (self.nargs != 1) + bool(self.multiple))
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/core.py”, line 1415, in _convert
return self.type(value, self, ctx)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/click/types.py”, line 39, in call
return self.convert(value, param, ctx)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/click/type.py”, line 79, in convert
return self._convert_primitive(value, param, ctx)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/click/type.py”, line 172, in _convert_primitive
return qiime2.sdk.util.parse_primitive(self.type_expr, value)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/core/type/util.py”, line 213, in parse_primitive
result.append(_interrogate_types(allowed, v))
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/core/type/util.py”, line 170, in _interrogate_types
raise _COERCE_ERROR
ValueError: Could not coerce value based on expression provided.

thanks

You are missing a space here:

It should be:

--p-sampling-depth 36000 --m-metadata-file metadata.txt

Hope that helps!

1 Like

thanks, now it is working, silly mistake!

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