Funcotator - WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr....
REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
12:22:44.594 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000377837.5 for variant: chr1:6412417-6412418(AT* -> A): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000377837.5 Variant: [VC Unknown @ chr1:6412417-6412418 Q. of type=INDEL alleles=[AT*, A] attr={AS_FilterStatus=SITE, AS_SB_TABLE=[0, 0|0, 0], DP=1, ECNT=5, GERMQ=1, MBQ=[0, 30], MFRL=[0, 225], MMQ=[60, 60], MPOS=39, POPAF=1.28, RPA=[22, 21], RU=T, STR=true, STRQ=1, TLOD=4.20} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0 filters=clustered_events,germline,slippage
12:22:44.600 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000377837.5 for problem variant: chr1:6412417-6412418(AT* -> A)
12:22:46.360 INFO ProgressMeter - chr1:7546157 0.2 3000 14771.0
12:22:56.769 INFO ProgressMeter - chr1:15441040 0.4 6000 15932.0
12:23:08.615 INFO ProgressMeter - chr1:24268222 0.6 10000 17420.6
12:23:18.806 INFO ProgressMeter - chr1:32245507 0.7 13000 17475.9
12:23:29.190 INFO ProgressMeter - chr1:40884137 0.9 16000 17449.2
12:23:40.060 INFO ProgressMeter - chr1:49383659 1.1 19000 17302.6
12:23:52.381 INFO ProgressMeter - chr1:59695584 1.3 23000 17645.3
12:24:03.424 INFO ProgressMeter - chr1:68377682 1.5 27000 18151.3
12:24:13.590 INFO ProgressMeter - chr1:76887474 1.7 31000 18709.1
12:24:25.294 INFO ProgressMeter - chr1:85925943 1.9 36000 19438.3
12:24:35.871 INFO ProgressMeter - chr1:94465524 2.0 40000 19721.1
12:24:46.052 INFO ProgressMeter - chr1:102403847 2.2 44000 20018.4
12:24:57.807 INFO ProgressMeter - chr1:111078655 2.4 49000 20468.7
12:25:09.216 INFO ProgressMeter - chr1:120476481 2.6 53000 20510.4
12:25:20.032 INFO ProgressMeter - chr1:148975263 2.8 57000 20620.0
12:25:23.276 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000420382.1 for variant: chr1:151765708-151765710(ATT* -> A): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000420382.1 Variant: [VC Unknown @ chr1:151765708-151765710 Q. of type=INDEL alleles=[ATT*, A] attr={AS_FilterStatus=weak_evidence, AS_SB_TABLE=[0, 0|0, 0], DP=1, ECNT=1, GERMQ=1, MBQ=[0, 30], MFRL=[0, 325], MMQ=[60, 60], MPOS=29, POPAF=0.839, RPA=[15, 13], RU=T, STR=true, STRQ=93, TLOD=3.31} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,0,1 filters=germline,weak_evidence
12:25:23.277 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000420382.1 for problem variant: chr1:151765708-151765710(ATT* -> A)
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The provided error message is quite different from what you have observed in the other thread and github. The case here is a limitation of Funcotator version that you are using. Can you provide us more details about which version you are using?
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Hello sir, Gökalp Çelik
Upon checking, I'm using Funcotator integrated within GATK version 4.5.0.0.
gatk Funcotator --version
Using GATK jar /home/user/miniconda3/envs/gatk_env/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/user/miniconda3/envs/gatk_env/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar Funcotator --version
The Genome Analysis Toolkit (GATK) v4.5.0.0
HTSJDK Version: 4.1.0
Picard Version: 3.1.1Best regards,
FATIMA ZOHRA ATTOUAHRI -
The error message shown here is quite clear about the current state of the code and your tool will continue normally to annotate other variants but just for this site you will get a default funcotation string. We do have PR's prepared to change this behavior of Funcotator but they are not ready for prime time soon so it will take some time to get it going.
I hope this helps.
Regards.
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