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refinem ssu_erroneous error #28

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zhaohuicheng opened this issue Oct 8, 2018 · 2 comments
Open

refinem ssu_erroneous error #28

zhaohuicheng opened this issue Oct 8, 2018 · 2 comments

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@zhaohuicheng
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when i use this command:
refinem ssu_erroneous -x fasta maxbin3/ taxon_profile_output_dir3/ ~/biosoft/diamond-master/gtdb_r80_ssu_db.2018-01-18.fna ~/biosoft/checkM/RefineM-master/RefineM-master/gtdb_r80_taxonomy.2017-12-15.tsv ssu_output_dir
[2018-10-08 13:35:28] INFO: RefineM v0.0.24
[2018-10-08 13:35:28] INFO: refinem ssu_erroneous -x fasta maxbin3/ taxon_profile_output_dir3/ /home/liu507/biosoft/diamond-master/gtdb_r80_ssu_db.2018-01-18.fna /home/liu507/biosoft/checkM/RefineM-master/RefineM-master/gtdb_r80_taxonomy.2017-12-15.tsv ssu_output_dir
[2018-10-08 13:35:28] INFO: Identifying SSU rRNA genes.
[2018-10-08 13:43:37] INFO: Extracting SSU rRNA genes.
[2018-10-08 13:43:37] INFO: Classifying SSU rRNA genes.
[2018-10-08 13:44:05] INFO: Identifying scaffolds with 16S rRNA genes with divergent taxonomic classification.

Unexpected error: <type 'exceptions.KeyError'>
Traceback (most recent call last):
File "/usr/local/bin/refinem", line 4, in
import('pkg_resources').run_script('refinem==0.0.24', 'refinem')
File "/home/liu507/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 658, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/liu507/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 1438, in run_script
exec(code, namespace, namespace)
File "/usr/local/lib/python2.7/dist-packages/refinem-0.0.24-py2.7.egg/EGG-INFO/scripts/refinem", line 396, in
parser.parse_options(args)
File "/usr/local/lib/python2.7/dist-packages/refinem-0.0.24-py2.7.egg/refinem/main.py", line 686, in parse_options
self.ssu_erroneous(options)
File "/usr/local/lib/python2.7/dist-packages/refinem-0.0.24-py2.7.egg/refinem/main.py", line 334, in ssu_erroneous
options.output_dir)
File "/usr/local/lib/python2.7/dist-packages/refinem-0.0.24-py2.7.egg/refinem/ssu.py", line 537, in erroneous
if r not in common_taxa[gid]:
KeyError: '0179.maxbin.041'

@ddeemerpurdue
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I am also getting this error. Haven't taken a deep dive into what's going on but at first glance not sure what is going on? Thank you.

@donovan-h-parks
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Hi. Do you have a set of data (ideally small) you can send me that produced this error? Thanks.

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3 participants