How to Remove identifier from Sequence Reference?

Hi all,
I used sequence and taxonomy references for a functional gene. It generated an error in Vsearch.

Plugin error from feature-classifier:

’Identifier 442 was reported in taxonomic search results, but was not present in the reference taxonomy.'

In the sequence reference file there is no number list beside the ids that then I remove the identifier 442 from sequence reference which is not present in taxonomy reference.

Do you have any idea to solve such a problem?

I use Qiime2 Version 2020.08.

qiime feature-classifier classify-consensus-vsearch \

–i-query 3merged-Rep.Seq-mcrA-DNA.qza
–i-reference-reads mothur-Ref-sequences.qza
–i-reference-taxonomy Mothur-Re-fTaxonomy.qza
–p-maxaccepts 100
–p-perc-identity 0.90
–p-strand plus
–p-maxhits all
–p-threads 200
–p-unassignable-label unassigned
–o-classification Blast-Mothur-mcrA-DNA-80%.qza
–verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --usearch_global /tmp/qiime2-archive-6rio6iv6/7f74dce4-3cc2-42b9-b512-dee6afeefd0a/data/dna-sequences.fasta --id 0.9 --query_cov 0.8 --strand plus --maxaccepts 100 --maxrejects 0 --db /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/data/dna-sequences.fasta --threads 200 --output_no_hits --blast6out /tmp/tmpelvsl_9r

vsearch v2.7.0_linux_x86_64, 503.8GB RAM, 56 cores

Reading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file 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/tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/dReading file /tmp/qiime2-archive-qilfndux/74e121fa-d85b-4260-8933-fe9a0b07b3fe/data/dna-sequences.fasta 100%
3603404 nt in 8135 seqs, min 390, max 471, avg 443
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching query sequences: 799 of 804 (99.38%)
Traceback (most recent call last):
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pandas/core/indexes/base.py”, line 4736, in get_value
return libindex.get_value_box(s, key)
File “pandas/_libs/index.pyx”, line 51, in pandas._libs.index.get_value_box
File “pandas/_libs/index.pyx”, line 47, in pandas._libs.index.get_value_at
File “pandas/_libs/util.pxd”, line 98, in pandas._libs.util.get_value_at
File “pandas/_libs/util.pxd”, line 83, in pandas._libs.util.validate_indexer
TypeError: ‘str’ object cannot be interpreted as an integer

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py”, line 105, in import_blast_format_assignments
t = ref_taxa[id
]
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pandas/core/series.py”, line 1071, in getitem
result = self.index.get_value(self, key)
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pandas/core/indexes/base.py”, line 4744, in get_value
raise e1
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pandas/core/indexes/base.py”, line 4730, in get_value
return self._engine.get_value(s, k, tz=getattr(series.dtype, “tz”, None))
File “pandas/_libs/index.pyx”, line 80, in pandas._libs.index.IndexEngine.get_value
File “pandas/_libs/index.pyx”, line 88, in pandas._libs.index.IndexEngine.get_value
File “pandas/_libs/index.pyx”, line 131, in pandas._libs.index.IndexEngine.get_loc
File “pandas/_libs/hashtable_class_helper.pxi”, line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item
File “pandas/_libs/hashtable_class_helper.pxi”, line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: ‘442’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in classify_consensus_vsearch
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_classifier/_vsearch.py”, line 64, in classify_consensus_vsearch
unassignable_label=unassignable_label)
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py”, line 30, in _consensus_assignments
output.name, ref_taxa, unassignable_label=unassignable_label)
File “/home/rabiei/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py”, line 110, in import_blast_format_assignments
‘taxonomy.’).format(str(id
)))
KeyError: ‘Identifier 442 was reported in taxonomic search results, but was not present in the reference taxonomy.’

Plugin error from feature-classifier:

‘Identifier 442 was reported in taxonomic search results, but was not present in the reference taxonomy.’

See above for debug info.

Thanks

Qiimer

Hi @TurboQiimer,

It looks like this error can crop up for a number of reasons. I suggest starting by consulting the following two posts:

This should give you a good idea of where to start investigating the source of the issue in your particular case. If you don’t have any luck with the previously discussed solutions (you may find others as well by searching the forum) then feel free to report back here. If you can, share the files you are working with as this issue seems to be highly dependent on the specific files you’re working with.

1 Like

Hi @andrewsanchez

Thanks a lot for the reply.

I ran the first command from this thread.

The command: grep '^>' mcrAtemplate.fasta | tr -d '>' | cat - tax4mcrA.taxonomy | grep -v ';' | sort | uniq -u

But there are many IDs shown!

I do not know the IDs are present in taxonomy file or not! and I do not know I should remove all or not! If yes, there are many IDs, so removing them manually takes much more time.

Could you please give me an idea?

Thanks
Qiiimer

Dear @andrewsanchez
Hi, if it is possible, please accelerate in replying me. I have other database then I need to follow your instruction and apply for others.
Have great moments ahead.
Thanks
Qiimer