Funocator not moving along traversal
Hi,
I'm trying to run the somatic variant calling pipeline. I've gotten to the funocator step but when I run funocator it never moves along the traversal. I'm not sure if the information its giving is relevant and I'm not sure what else to try. Do you have any idea why its not moving or what I should be doing to look into it?
REQUIRED for all errors and issues:
a) GATK version used:
v4.5.0.0
b) Exact command used:
gatk Funcotator -variant ../out/Filter_mutect/G1_2nM_BL_raw_variants.vcf \
--reference /export/home/bin/genomes/BWA_hg38/Homo_sapiens_assembly38.fasta \
--ref-version hg38 \
--data-sources-path /export/home/bin/variant_calling/funcotator_dataSources.v1.8.hg38.20230908s \
--output ../out/Annotate_variants/G1_2nM_BL_raw_variants.vcf \
--output-file-format VCF
c) Entire program log:
16:21:32.752 INFO Funcotator - Initializing Funcotator Engine...
16:21:32.762 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required.
16:21:32.764 INFO FuncotatorUtils - Input VCF has been determined to not based on b37:
16:21:32.764 INFO FuncotatorUtils - The following contigs are present in b37 and missing in the input VCF sequence dictionary:
16:21:32.767 INFO FuncotatorUtils - 1 (len=249250621,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 2 (len=243199373,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 3 (len=198022430,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 4 (len=191154276,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 5 (len=180915260,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 6 (len=171115067,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 7 (len=159138663,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 8 (len=146364022,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 9 (len=141213431,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 10 (len=135534747,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 11 (len=135006516,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 12 (len=133851895,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 13 (len=115169878,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 14 (len=107349540,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 15 (len=102531392,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 16 (len=90354753,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 17 (len=81195210,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 18 (len=78077248,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 19 (len=59128983,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 20 (len=63025520,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 21 (len=48129895,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 22 (len=51304566,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - X (len=155270560,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - Y (len=59373566,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - MT (len=16569,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000207.1 (len=4262,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000226.1 (len=15008,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000229.1 (len=19913,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000231.1 (len=27386,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000210.1 (len=27682,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000239.1 (len=33824,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000235.1 (len=34474,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000201.1 (len=36148,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000247.1 (len=36422,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000245.1 (len=36651,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000197.1 (len=37175,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000203.1 (len=37498,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000246.1 (len=38154,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000249.1 (len=38502,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000196.1 (len=38914,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000248.1 (len=39786,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000244.1 (len=39929,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000238.1 (len=39939,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000202.1 (len=40103,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000234.1 (len=40531,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000232.1 (len=40652,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000206.1 (len=41001,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000240.1 (len=41933,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000236.1 (len=41934,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000241.1 (len=42152,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000243.1 (len=43341,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000242.1 (len=43523,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000230.1 (len=43691,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000237.1 (len=45867,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000233.1 (len=45941,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000204.1 (len=81310,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000198.1 (len=90085,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000208.1 (len=92689,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000191.1 (len=106433,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000227.1 (len=128374,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000228.1 (len=129120,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000214.1 (len=137718,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000221.1 (len=155397,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000209.1 (len=159169,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000218.1 (len=161147,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000220.1 (len=161802,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000213.1 (len=164239,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000211.1 (len=166566,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000199.1 (len=169874,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000217.1 (len=172149,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000216.1 (len=172294,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000215.1 (len=172545,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000205.1 (len=174588,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000219.1 (len=179198,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000224.1 (len=179693,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000223.1 (len=180455,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000195.1 (len=182896,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000212.1 (len=186858,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000222.1 (len=186861,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000200.1 (len=187035,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000193.1 (len=189789,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000194.1 (len=191469,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000225.1 (len=211173,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000192.1 (len=547496,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - NC_007605 (len=171823,assembly=NC_007605.1)
16:21:32.774 INFO Funcotator - Creating a VCF file for output: file:/export/bioinfpog2/Mhairi/Hager/Analysis/DNA/hg38/bin/../out/Annotate_variants/G1_2nM_BL_raw_variants.vcf
16:21:32.825 INFO ProgressMeter - Starting traversal
16:21:32.826 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:21:32.762 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required.
16:21:32.764 INFO FuncotatorUtils - Input VCF has been determined to not based on b37:
16:21:32.764 INFO FuncotatorUtils - The following contigs are present in b37 and missing in the input VCF sequence dictionary:
16:21:32.767 INFO FuncotatorUtils - 1 (len=249250621,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 2 (len=243199373,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 3 (len=198022430,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 4 (len=191154276,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 5 (len=180915260,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 6 (len=171115067,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 7 (len=159138663,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 8 (len=146364022,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 9 (len=141213431,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 10 (len=135534747,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 11 (len=135006516,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 12 (len=133851895,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 13 (len=115169878,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 14 (len=107349540,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 15 (len=102531392,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 16 (len=90354753,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 17 (len=81195210,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 18 (len=78077248,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 19 (len=59128983,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 20 (len=63025520,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 21 (len=48129895,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 22 (len=51304566,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - X (len=155270560,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - Y (len=59373566,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - MT (len=16569,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000207.1 (len=4262,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000226.1 (len=15008,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000229.1 (len=19913,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000231.1 (len=27386,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000210.1 (len=27682,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000239.1 (len=33824,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000235.1 (len=34474,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000201.1 (len=36148,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000247.1 (len=36422,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000245.1 (len=36651,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - GL000197.1 (len=37175,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000203.1 (len=37498,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000246.1 (len=38154,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000249.1 (len=38502,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000196.1 (len=38914,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000248.1 (len=39786,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000244.1 (len=39929,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000238.1 (len=39939,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000202.1 (len=40103,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000234.1 (len=40531,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000232.1 (len=40652,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000206.1 (len=41001,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000240.1 (len=41933,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000236.1 (len=41934,assembly=GRCh37)
16:21:32.770 INFO FuncotatorUtils - GL000241.1 (len=42152,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000243.1 (len=43341,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000242.1 (len=43523,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000230.1 (len=43691,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000237.1 (len=45867,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000233.1 (len=45941,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000204.1 (len=81310,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000198.1 (len=90085,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000208.1 (len=92689,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000191.1 (len=106433,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000227.1 (len=128374,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000228.1 (len=129120,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000214.1 (len=137718,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000221.1 (len=155397,assembly=GRCh37)
16:21:32.771 INFO FuncotatorUtils - GL000209.1 (len=159169,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000218.1 (len=161147,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000220.1 (len=161802,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000213.1 (len=164239,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000211.1 (len=166566,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000199.1 (len=169874,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000217.1 (len=172149,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000216.1 (len=172294,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000215.1 (len=172545,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000205.1 (len=174588,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000219.1 (len=179198,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000224.1 (len=179693,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000223.1 (len=180455,assembly=GRCh37)
16:21:32.772 INFO FuncotatorUtils - GL000195.1 (len=182896,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000212.1 (len=186858,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000222.1 (len=186861,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000200.1 (len=187035,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000193.1 (len=189789,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000194.1 (len=191469,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000225.1 (len=211173,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - GL000192.1 (len=547496,assembly=GRCh37)
16:21:32.773 INFO FuncotatorUtils - NC_007605 (len=171823,assembly=NC_007605.1)
16:21:32.774 INFO Funcotator - Creating a VCF file for output: file:/export/bioinfpog2/Mhairi/Hager/Analysis/DNA/hg38/bin/../out/Annotate_variants/G1_2nM_BL_raw_variants.vcf
16:21:32.825 INFO ProgressMeter - Starting traversal
16:21:32.826 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
-
(Answered in the user's other thread here: https://gatk.broadinstitute.org/hc/en-us/community/posts/24087106721051-Funocator-chromosome-missmatch-to-somatic-variant-calling-pipeline)
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