Question: Oncotator v1.8.0.0 usage, download database.
0
gravatar for Peavil
23 months ago by
Peavil10
Peavil10 wrote:

Hi.

I used oncotator v1.8.0.0 with old-version database,

It was running well.

But, when I downloaded new database(oncotator_v1_ds_April052016.tar.gz. ) at (http://gatkforums.broadinstitute.org/gatk/discussion/4154/howto-install-and-run-oncotator-for-the-first-time),

It doesn't run, and then print error code.

2017-01-11 14:13:42,591 INFO [oncotator.datasources.EnsemblTranscriptDatasource:109] GENCODE v19 is being setth basic filtering. Traceback (most recent call last): File "/tools/Python/Python-2.7.8/bin/Oncotator", line 9, in <module> load_entry_point('Oncotator==v1.8.0.0', 'console_scripts', 'Oncotator')() File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Oncotat, line 305, in main other_opts=other_opts, annotating_type=annotating_type) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/utils/RificationFactory.py", line 113, in create_run_spec datasource_list = DatasourceFactory.createDatasources(datasource_dir, genomeBuild, isMulticore=is_multicomCores=num_cores, tx_mode=tx_mode) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Datasoutory.py", line 294, in createDatasources result = DatasourceFactory._createDatasourcesMulticore(numCores, dsQueueList) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Datasoutory.py", line 317, in _createDatasourcesMulticore result.append(DatasourceFactory.createDatasourceGivenTuple(dsTuple))
File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Datasoutory.py", line 106, in createDatasourceGivenTuple return DatasourceFactory.createDatasource(configTuple[0], configTuple[1]) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Datasoutory.py", line 100, in createDatasource return DatasourceFactory.createDatasourceFromConfigParser(configParser, leafDir) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Datasoutory.py", line 186, in createDatasourceFromConfigParser match_mode=configParser.get('general', 'match_mode')) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/datasouabixIndexedVcfDatasource.py", line 84, in __init__ self.vcf_reader = vcf.Reader(filename=src_file, strict_whitespace=True) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7-linux-x86_64.egg/vcf/parser.ine 283, in __init__ self._parse_metainfo() File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7-linux-x86_64.egg/vcf/parser.ine 304, in _parse_metainfo key, val = parser.read_info(line) File "/tools/Python/Python-2.7.8/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7-linux-x86_64.egg/vcf/parser.ine 118, in read_info "One of the INFO lines is malformed: %s" % info_string) SyntaxError: One of the INFO lines is malformed: INFO=<id=dp_hist,number=r,type=string,description="histogr dp;="" mids:="" 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5"<="" p="">

When I tried same command with old-version db, it still runs and result output.

How do I adjust this problem?

(my old version db is oncotator_v1_ds_Jan262015.)

tool broad oncotator database • 1.1k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by Peavil10
0
gravatar for Peavil
23 months ago by
Peavil10
Peavil10 wrote:

I could solve the problem. That's because I did not install Oncotator properly. After installing Oncotator properly, I was able to run the program with the new DB.

ADD COMMENTlink written 23 months ago by Peavil10
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