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Empty VCF generated after using Mutect2

JaspreetJaspreet Cleveland, OHMember

I tried running Mutect2 on tumor and matched-normal bam files for calling somatic mutations and after processing of 24hrs, I received an empty .vcf file along with index file (vcf.idx) of 27K.
Here is the code I am using:

java -jar ~/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T MuTect2 -R ~/hg19.fa -I:tumor ~/output/base_recalibration/tumor.calibrated.bam -I:normal ~/output/base_recalibration/normal.calibrated.bam --dbsnp ~/Merged_dbsnp.vcf.gz -o ~/output/mutect2_out/output.vcf

Below is a part of console output while running code, My major concern is with microscheduler which shows 0 reads filtered:

INFO 11:02:16,954 ProgressMeter - chrX:2990504 2.881033286E9 21.7 h 27.0 s 93.2% 23.3 h 95.4 m
INFO 11:03:16,956 ProgressMeter - chrX:8538916 2.881033286E9 21.7 h 27.0 s 93.3% 23.2 h 92.8 m
INFO 11:04:16,957 ProgressMeter - chrX:11308883 2.881033286E9 21.7 h 27.0 s 93.4% 23.2 h 91.6 m
INFO 11:05:16,958 ProgressMeter - chrX:13786528 2.881033286E9 21.7 h 27.0 s 93.5% 23.2 h 90.5 m
INFO 11:06:16,959 ProgressMeter - chrX:16196392 2.881033286E9 21.7 h 27.0 s 93.6% 23.2 h 89.4 m
INFO 11:07:26,959 ProgressMeter - chrX:18800835 2.881033286E9 21.8 h 27.0 s 93.7% 23.2 h 88.2 m
INFO 11:08:26,960 ProgressMeter - chrX:19725479 2.881033286E9 21.8 h 27.0 s 93.7% 23.2 h 87.8 m
INFO 11:09:26,961 ProgressMeter - chrX:21861651 2.881033286E9 21.8 h 27.0 s 93.8% 23.2 h 86.9 m
INFO 11:10:26,962 ProgressMeter - chrX:23411727 2.881033286E9 21.8 h 27.0 s 93.8% 23.2 h 86.2 m
INFO 11:11:26,963 ProgressMeter - chrX:27479727 2.881033286E9 21.8 h 27.0 s 94.0% 23.2 h 84.3 m
INFO 11:12:36,964 ProgressMeter - chrX:30726448 2.881033286E9 21.8 h 27.0 s 94.1% 23.2 h 82.8 m
INFO 11:13:36,965 ProgressMeter - chrX:32328723 2.881033286E9 21.9 h 27.0 s 94.1% 23.2 h 82.1 m
INFO 11:14:36,966 ProgressMeter - chrX:32632867 2.881033286E9 21.9 h 27.0 s 94.1% 23.2 h 82.0 m
INFO 11:15:46,967 ProgressMeter - chrX:37663546 2.881033286E9 21.9 h 27.0 s 94.3% 23.2 h 79.7 m
INFO 11:16:57,050 ProgressMeter - chrX:39913962 2.881033286E9 21.9 h 27.0 s 94.4% 23.2 h 78.7 m
INFO 11:17:57,051 ProgressMeter - chrX:41026993 2.881033286E9 21.9 h 27.0 s 94.4% 23.2 h 78.2 m
INFO 11:19:07,056 ProgressMeter - chrX:43603443 2.881033286E9 22.0 h 27.0 s 94.5% 23.2 h 77.0 m
INFO 11:20:17,057 ProgressMeter - chrX:45493032 2.881033286E9 22.0 h 27.0 s 94.5% 23.2 h 76.2 m
INFO 11:21:27,057 ProgressMeter - chrX:47775126 2.881033286E9 22.0 h 27.0 s 94.6% 23.2 h 75.2 m
INFO 11:22:27,058 ProgressMeter - chrX:48826508 2.881033286E9 22.0 h 27.0 s 94.6% 23.3 h 74.8 m
INFO 11:23:27,059 ProgressMeter - chrX:49855697 2.881033286E9 22.0 h 27.0 s 94.7% 23.3 h 74.3 m
INFO 11:24:37,059 ProgressMeter - chrX:52685953 2.881033286E9 22.0 h 27.0 s 94.8% 23.3 h 73.0 m
INFO 11:25:37,060 ProgressMeter - chrX:53574010 2.881033286E9 22.1 h 27.0 s 94.8% 23.3 h 72.7 m
INFO 11:26:37,061 ProgressMeter - chrX:54325065 2.881033286E9 22.1 h 27.0 s 94.8% 23.3 h 72.4 m
INFO 11:27:47,062 ProgressMeter - chrX:61945183 2.881033286E9 22.1 h 27.0 s 95.1% 23.2 h 68.8 m
INFO 11:28:47,062 ProgressMeter - chrX:67765142 2.881033286E9 22.1 h 27.0 s 95.3% 23.2 h 66.1 m
INFO 11:29:47,063 ProgressMeter - chrX:69720649 2.881033286E9 22.1 h 27.0 s 95.3% 23.2 h 65.2 m
INFO 11:30:57,064 ProgressMeter - chrX:70830887 2.881033286E9 22.2 h 27.0 s 95.4% 23.2 h 64.8 m
INFO 11:31:57,064 ProgressMeter - chrX:73042497 2.881033286E9 22.2 h 27.0 s 95.4% 23.2 h 63.8 m
INFO 11:32:57,065 ProgressMeter - chrX:73070963 2.881033286E9 22.2 h 27.0 s 95.4% 23.2 h 63.8 m
INFO 11:34:07,066 ProgressMeter - chrX:74965753 2.881033286E9 22.2 h 27.0 s 95.5% 23.3 h 63.0 m
INFO 11:35:17,066 ProgressMeter - chrX:76939080 2.881033286E9 22.2 h 27.0 s 95.6% 23.3 h 62.1 m
INFO 11:36:17,067 ProgressMeter - chrX:79283838 2.881033286E9 22.2 h 27.0 s 95.6% 23.3 h 61.0 m
INFO 11:37:27,068 ProgressMeter - chrX:81000487 2.881033286E9 22.3 h 27.0 s 95.7% 23.3 h 60.3 m
INFO 11:38:37,068 ProgressMeter - chrX:85340693 2.881033286E9 22.3 h 27.0 s 95.8% 23.3 h 58.3 m
INFO 11:39:37,069 ProgressMeter - chrX:95817023 2.881033286E9 22.3 h 27.0 s 96.2% 23.2 h 53.4 m
INFO 11:40:47,070 ProgressMeter - chrX:100356454 2.881033286E9 22.3 h 27.0 s 96.3% 23.2 h 51.3 m
INFO 11:41:57,070 ProgressMeter - chrX:101035790 2.881033286E9 22.3 h 27.0 s 96.3% 23.2 h 51.1 m
INFO 11:42:57,071 ProgressMeter - chrX:104993012 2.881033286E9 22.4 h 27.0 s 96.5% 23.2 h 49.3 m
INFO 11:43:57,078 ProgressMeter - chrX:107170443 2.881033286E9 22.4 h 27.0 s 96.5% 23.2 h 48.3 m
INFO 11:45:07,078 ProgressMeter - chrX:109561282 2.881033286E9 22.4 h 27.0 s 96.6% 23.2 h 47.2 m
INFO 11:46:07,079 ProgressMeter - chrX:112066444 2.881033286E9 22.4 h 27.0 s 96.7% 23.2 h 46.1 m
INFO 11:47:07,218 ProgressMeter - chrX:117744629 2.881033286E9 22.4 h 28.0 s 96.9% 23.1 h 43.5 m
INFO 11:48:07,218 ProgressMeter - chrX:119388408 2.881033286E9 22.4 h 28.0 s 96.9% 23.2 h 42.8 m
INFO 11:49:07,219 ProgressMeter - chrX:122599940 2.881033286E9 22.5 h 28.0 s 97.0% 23.1 h 41.3 m
INFO 11:50:17,220 ProgressMeter - chrX:128650073 2.881033286E9 22.5 h 28.0 s 97.2% 23.1 h 38.5 m
INFO 11:51:17,220 ProgressMeter - chrX:129215570 2.881033286E9 22.5 h 28.0 s 97.2% 23.1 h 38.3 m
INFO 11:52:17,221 ProgressMeter - chrX:131216772 2.881033286E9 22.5 h 28.0 s 97.3% 23.1 h 37.4 m
INFO 11:53:27,221 ProgressMeter - chrX:133627972 2.881033286E9 22.5 h 28.0 s 97.4% 23.1 h 36.3 m
INFO 11:54:27,222 ProgressMeter - chrX:135080614 2.881033286E9 22.5 h 28.0 s 97.4% 23.1 h 35.7 m
INFO 11:55:27,223 ProgressMeter - chrX:136067634 2.881033286E9 22.6 h 28.0 s 97.5% 23.1 h 35.3 m
INFO 11:56:37,224 ProgressMeter - chrX:144904366 2.881033286E9 22.6 h 28.0 s 97.7% 23.1 h 31.2 m
INFO 11:57:37,224 ProgressMeter - chrX:148564609 2.881033286E9 22.6 h 28.0 s 97.9% 23.1 h 29.6 m
INFO 11:58:37,225 ProgressMeter - chrX:151129789 2.881033286E9 22.6 h 28.0 s 97.9% 23.1 h 28.4 m
INFO 11:59:37,227 ProgressMeter - chrX:153236463 2.881033286E9 22.6 h 28.0 s 98.0% 23.1 h 27.5 m
INFO 12:00:37,228 ProgressMeter - chrX:153994088 2.881033286E9 22.6 h 28.0 s 98.0% 23.1 h 27.2 m
INFO 12:01:47,228 ProgressMeter - chrX:154508832 2.881033286E9 22.7 h 28.0 s 98.1% 23.1 h 26.9 m
INFO 12:02:47,229 ProgressMeter - chrY:59019329 3.036303846E9 22.7 h 26.0 s 100.0% 22.7 h 9.0 s
INFO 12:03:47,230 ProgressMeter - chrM:8870 3.095677412E9 22.7 h 26.0 s 100.0% 22.7 h 0.0 s
INFO 12:04:32,300 VectorLoglessPairHMM - Time spent in setup for JNI call : 23.940732500000003
INFO 12:04:32,301 PairHMM - Total compute time in PairHMM computeLikelihoods() : 51474.309994685005
INFO 12:04:32,301 MuTect2 - Ran local assembly on 4771 active regions
INFO 12:04:32,596 ProgressMeter - done 3.095693983E9 22.7 h 26.0 s 100.0% 22.7 h 0.0 s
INFO 12:04:32,596 ProgressMeter - Total runtime 81766.05 secs, 1362.77 min, 22.71 hours
INFO 12:04:32,597 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 69571980 total reads (0.00%)
INFO 12:04:32,597 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 12:04:32,597 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 12:04:32,597 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 12:04:32,598 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 12:04:32,598 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 12:04:32,598 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 12:04:32,598 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 12:04:40,333 GATKRunReport - Uploaded run statistics report to AWS S3

Can you please explain if anything is wrong in my code and how should I fix it?

Best Answer

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