Bug Description
Underscores in Sample IDs are not supported in deblur. This breaks in several ways --- the reference database check is unable to find any hits when there are underscores present in IDs. As well, IDs with underscores appear to be truncated when underscores are present.
Steps to reproduce the behavior
Run denoise-16s with samples with underscores in the IDs.
Expected behavior
Deblur should work as advertised.
Screenshots
A user reported that mock community samples were producing the following results:
Note sample HMP_mock_2 has no reads hitting the reference. The user had previously used the same mock community and had had success, so this reference miss was surprising.
I reran the same samples through denoise-16s using underscore-less sample IDs:
The sample in question now has the expected amount of reads hitting the reference.
Computation Environment
OS: macOS High Sierra
QIIME 2 Release: 2018.6
Questions
Perhaps the way to solve this in this plugin is to test sample IDs for underscores and error out when observed. Thoughts?
thermokarst
commented
6 years ago
Bug Description Underscores in Sample IDs are not supported in
deblur. This breaks in several ways --- the reference database check is unable to find any hits when there are underscores present in IDs. As well, IDs with underscores appear to be truncated when underscores are present.Steps to reproduce the behavior
denoise-16swith samples with underscores in the IDs.Expected behavior Deblur should work as advertised.
Screenshots A user reported that mock community samples were producing the following results:
Note sample
HMP_mock_2has no reads hitting the reference. The user had previously used the same mock community and had had success, so this reference miss was surprising.I reran the same samples through
denoise-16susing underscore-less sample IDs:The sample in question now has the expected amount of reads hitting the reference.
Computation Environment
Questions
References