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@mwong I think v18.104.22.168 fixes this issue.
@sherey65 Yes, removing the dbSNP annotations in the input file should eliminate the issue. As per the TCGA MAF spec, Reference_Allele and Tumor_Seq_Allele1 should be the same. If Tumor_Seq_Allele1 is the same as Tumor_Seq_Allele2, then you should…
@corlagon 1) Good catch. Under the hood, there is a minor issue: We set the datasource to CANONICAL during the first stage of initialization (thereby triggering the log messages) before setting to the user selection. You can just look at the las…
If you upgrade to Oncotator 22.214.171.124, I believe this issue has been fixed. @asoskins said: Hello, I've installed oncotator/126.96.36.199 and try to run it with python/2.7.3 on my vcf files with the following command line: oncotator -i VCF --db-…
@JeremyS Did you use the create_oncotator_venv.sh script to create a virtual environment and run oncotator from there?
@chung2000 Anything not listed here gets a score of 25. With lincRNA, there is usually no transcripts to contradict and an IGR result is impossible since it overlapped a transcript.
@np3 For a different project, I just got the same error as you and I just ran pip uninstall distribute and it worked.
@np3 Though I have newer packages that is very similar to my configuration. Usually the issue here is an incompatible version of distribute or setuptools with the version of python. Are you using a virtual environment? In other words, did you run…
@chung2000 @Geraldine_VdAuwera I have posted the Sept 17 corpus here.
@np3 I have been using Ubuntu 12.04 with no issues. Also, what version of python are you using?
@np3 Can you post the results of "pip freeze" ?
@np3 Try "pip install -U distribute" That has fixed this in the past.
--omitIntervalStatistics got rid of the error. Thanks!
Apologies for the poor markdown