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What does an error message mean?
Geraldine_VdAuwera
Cambridge, MAMember, Administrator, Broadie admin
Overview
This document lists error messages that you may encounter when using Oncotator. For each, you will find an explanation of what the error message means, and how to solve the problem (if possible).
Entrez Gene ID was zero, but Hugo Symbol was not Unknown
Problem: The current GENCODE datasource does not have a complete list of the Entrez Gene IDs.
Solution There is no solution yet. This is a known issue and will be solved in a future release of the default datasource corpus.
oncotator.DuplicateAnnotationException.DuplicateAnnotationException: 'Attempting to create an annotation multiple times
Problem: This occurs when Oncotator is being directed to create the same annotation on a mutation, but each with different values. Typically, this is caused by a maflite/tsv input file with redundant columns. For example, "Start_Position" and "start". Oncotator does use aliases, so the annotation could have different column header text, but be regarded as the same annotation.
Solution: You need to clean up the columns in your input file to avoid such conflicts.
Comments
****What does this error mean?****
please, help me.
=====================================================================================
Verbose mode on
Path:
['/usr/bin', '/usr/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg', '/usr/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg', '/usr/lib/python2.7/site-packages/enum34-1.0.4-py2.7.egg', '/usr/lib/python2.7/site-packages/more_itertools-2.2-py2.7.egg', '/usr/lib/python2.7/site-packages/natsort-3.5.2-py2.7.egg', '/usr/lib/python2.7/site-packages/python_memcached-1.53-py2.7.egg', '/usr/lib/python2.7/site-packages/nose-1.3.4-py2.7.egg', '/usr/lib/python2.7/site-packages/SQLAlchemy-0.9.8-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/shove-0.5.6-py2.7.egg', '/usr/lib/python2.7/site-packages/Cython-0.22-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/biopython-1.65-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/pandas-0.15.2-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/pysam-0.7.5-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/bcbio_gff-0.6.2-py2.7.egg', '/usr/lib/python2.7/site-packages/stuf-0.9.4-py2.7.egg', '/usr/lib/python2.7/site-packages/futures-2.2.0-py2.7.egg', '/usr/lib/python2.7/site-packages/python_dateutil-2.4.0-py2.7.egg', '/usr/lib/python2.7/site-packages/parse-1.4.1-py2.7.egg', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages']
2015-03-04 17:13:09,050 INFO [oncotator.Oncotator:235] Oncotator v1.5.1.0
2015-03-04 17:13:09,051 INFO [oncotator.Oncotator:236] WARNING [oncotator.DatasourceFactory:260] %s does not exist, so there will be no datasources.
2015-03-04 17:13:09,056 WARNING [oncotator.Annotator:466] THERE ARE NO DATASOURCES REGISTERED
2015-03-04 17:13:09,454 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 1000 mutations.
2015-03-04 17:13:09,849 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 2000 mutations.
2015-03-04 17:13:10,218 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 3000 mutations.
2015-03-04 17:13:10,556 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 4000 mutations.
2015-03-04 17:13:10,896 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 5000 mutations.
2015-03-04 17:13:11,242 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 6000 mutations.
2015-03-04 17:13:11,580 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 7000 mutations.
2015-03-04 17:13:11,926 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 8000 mutations.
2015-03-04 17:13:12,266 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 9000 mutations.
2015-03-04 17:13:12,611 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 10000 mutations.
2015-03-04 17:13:12,950 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 11000 mutations.
2015-03-04 17:13:13,293 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 12000 mutations.
2015-03-04 17:13:13,633 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 13000 mutations.
2015-03-04 17:13:13,970 INFO [oncotator.output.TcgaMafOutputRenderer:276] Rendered 14000 mutations.
2015-03-04 17:13:14,109 INFO [oncotator.output.TcgaMafOutputRenderer:288] Rendered all 14402 mutations.
It seems you did not provide a datasource to the program. What was your command line?
@Geraldine_VdAuwera Is there any work around for the "Entrez Gene ID was zero, but Hugo Symbol was not Unknown" issue?
Hi everyone!
I am trying to annotate my vcf file (prepared using GATK Best Practices workflow) using oncotator :
AND here is my command:
oncotator -v --log_name=oncotator.SNPs.log \
--input_format=VCF --output_format=VCF \
--db-dir=/seqdata/Oncotator_Datasource/oncotator_v1_ds_April052016 \
/nextera_rapid_capture_exome/varcall_filtered/SNPs.vcf \
/nextera_rapid_capture_exome/varcall_filtered/SNPs.oncotator.vcf hg19
I am getting the following error message:
...
2017-01-12 18:22:52,284 WARNING [oncotator.output.OutputDataManager:521] Annotation or config file specifying is not split for field type (INFO) with Number=A name: ExAC_Hom_SAS A datasource or VCF file may be misconfigured.
2017-01-12 18:22:52,284 WARNING [oncotator.output.OutputDataManager:521] Annotation or config file specifying is not split for field type (INFO) with Number=A name: ExAC_AC_Hemi A datasource or VCF file may be misconfigured.
2017-01-12 18:22:52,284 WARNING [oncotator.output.OutputDataManager:521] Annotation or config file specifying is not split for field type (INFO) with Number=A name: ExAC_clinvar_pathogenic A datasource or VCF file may be misconfigured.
2017-01-12 18:22:52,285 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.out.config). Trying configs/ prepend.
2017-01-12 18:22:52,285 INFO [oncotator.utils.ConfigUtils:199] Found config file (vcf.out.config) using configs/ prepend.
2017-01-12 18:22:52,287 INFO [oncotator.utils.SampleNameSelector:90] Sample name is in the sample_name column.
2017-01-12 18:23:02,769 INFO [oncotator.output.OutputDataManager:194] Wrote 1000 mutations to tsv.
2017-01-12 18:23:13,408 INFO [oncotator.output.OutputDataManager:194] Wrote 2000 mutations to tsv.
2017-01-12 18:23:25,661 INFO [oncotator.output.OutputDataManager:194] Wrote 3000 mutations to tsv.
2017-01-12 18:23:30,025 ERROR [oncotator.input.VcfInputMutationCreator:328] SPANNING DELETIONS ARE NOT SUPPORTED.
Traceback (most recent call last):
File "/storage/software/python-2.7.11/bin/oncotator", line 11, in
load_entry_point('Oncotator==1.10.0.0.dev0', 'console_scripts', 'oncotator')()
File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 309, in main
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 437, in annotate
File "build/bdist.linux-x86_64/egg/oncotator/output/VcfOutputRenderer.py", line 119, in renderMutations
File "build/bdist.linux-x86_64/egg/oncotator/output/OutputDataManager.py", line 92, in init
File "build/bdist.linux-x86_64/egg/oncotator/output/OutputDataManager.py", line 160, in _writeMuts2Tsv
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 448, in _applyManualAnnotations
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 456, in _applyDefaultAnnotations
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 504, in _annotate_mutations_using_datasources
File "build/bdist.linux-x86_64/egg/oncotator/input/VcfInputMutationCreator.py", line 329, in createMutations
oncotator.utils.OncotatorException.OncotatorException: Spanning deletions are not supported at this time.
Could you please help me with this?
Hi everyone!
I have finally found solution to this error message ( that I posted before):
here it is:
I have followed the error message 'File "build/bdist.linux-x86_64/egg/oncotator/input/VcfInputMutationCreator.py", line 329, in createMutations'
and checked this Python code in https://github.com/broadinstitute/oncotator/blob/develop/oncotator/input/VcfInputMutationCreator.py
and found that this ERROR is cased by the presence of '*' symbol in the ALT field: i.e. by the presence of spanning deletions
in my input VCF file
basically - this is what error message says )))
NOTE that use of SelectVariants with --selectTypeToExclude INDEL --selectTypeToExclude MIXED --selectTypeToExclude SYMBOLIC
will not remove * - spanning deletions
I have removed variants with spanning deletions (there were only few) using grep
check first manually - what is going to be removed:
zcat myfilename.vcf.gz | grep -E ',*|*,' | awk '{print $1,$2,$3,$4,$5,$6}' | more
remove *'s:
zcat myfilename.vcf.gz | grep -E --invert-match ',*|*,' > no_spanning_dels.vcf