I am using Mutect2 as suggested to variant call non-tumor samples consisting of multiple individuals that were pooled together and sequenced as one. This affects the ploidy value. However, FilterMutectCalls fails consistently, and skipping this step to hard filter using VariantFiltration results in vcfs where no variants pass the filters (namely the suggested QUAL > 30). I am unsure which step is failing, since all run "successfully" and this use case is not as common. From the other help forum postings, it seems like FilterMutectCalls may be unnecessary, and the alpha metric is for comparative tumor data, so I tried skipping this to go directly to VariantFiltration, but nothing passes.

a) GATK version used: 4.4.0

b) Exact command used: 

for Mutect2:

/global/scratch/users/laurenhamm/thesis/software/gatk/gatk --java-options "-Xmx64G" Mutect2\
    -R /global/scratch/users/laurenhamm/thesis/ref-genomes/v3_mt-cs/Mgut_v3_mt-cs.fa\
    -I /global/scratch/users/laurenhamm/thesis/aim2/paleomix/bamOuts/HOL_2015_pool.GEAsamples.bam\
    -O /global/scratch/users/laurenhamm/thesis/aim2/vcfs/GATK/indv_vcfs/Mutect2/HOL_2015_pool.M2.g.vcf.gz\
    -ERC GVCF\
    -ploidy 46 \
    --min-base-quality-score 25 \

for FilterMutectCalls:

/global/scratch/users/laurenhamm/thesis/software/gatk/gatk --java-options "-Xmx4g" FilterMutectCalls \
                -V $f \
                -R /global/scratch/users/laurenhamm/thesis/ref-genomes/v3_mt-cs/Mgut_v3_mt-cs.fa \
                --max-alt-allele-count 1 \
                --min-median-base-quality 20 \
                --min-median-mapping-quality 30 \
                --create-output-variant-index TRUE \
                -O FilterAnno/"$popName".FilterAnno.vcf.gz

for VariantFiltration/SelectVariants:

/global/scratch/users/laurenhamm/thesis/software/gatk/gatk --java-options "-Xmx4g" VariantFiltration \
                -V $f \
                -filter "QD < 2.0" --filter-name "QD2" \
                -filter "QUAL < 30.0" --filter-name "QUAL30" \
                -filter "SOR > 3.0" --filter-name "SOR3" \
                -filter "FS > 60.0" --filter-name "FS60" \
                -filter "MQ < 40" --filter-name "MQ40" \
                -filter "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \
                -filter "ReadPosRankSum < 8.0" --filter-name "ReadPosRankSum8" \
                -O FilterAnno/"$popName".M2.FilterAnno.vcf.gz

        /global/scratch/users/laurenhamm/thesis/software/gatk/gatk --java-options "-Xmx4g" SelectVariants \
        -V FilterAnno/"$popName".M2.FilterAnno.vcf.gz \
        -select-type SNP \
        --exclude-filtered \
        -O FilterAnno/"$popName".M2.FilterAnnp.pruned.vcf.gz

c) Entire program log:

for FilterMutectCalls:

Using GATK jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-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 -Xmx4g -jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar FilterMutectCalls -V BEL_2014_pool.M2.g.vcf.gz -R /global/scratch/users/laurenhamm/thesis/ref-genomes/v3_mt-cs/Mgut_v3_mt-cs.fa --max-alt-allele-count 1 --min-median-base-quality 20 --min-median-mapping-quality 30 --create-output-variant-index TRUE -O FilterAnno/BEL_2014_pool.FilterAnno.vcf.gz
18:26:03.573 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
18:26:03.815 INFO  FilterMutectCalls - ------------------------------------------------------------
18:26:03.820 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.4.0.0-43-gd79823f-SNAPSHOT
18:26:03.820 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
18:26:03.821 INFO  FilterMutectCalls - Executing as laurenhamm@n0001.savio2 on Linux v4.18.0-553.5.1.el8_10.x86_64 amd64
18:26:03.821 INFO  FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v22.0.1+8-16
18:26:03.821 INFO  FilterMutectCalls - Start Date/Time: December 3, 2024, 6:26:03 PM PST
18:26:03.821 INFO  FilterMutectCalls - ------------------------------------------------------------
18:26:03.821 INFO  FilterMutectCalls - ------------------------------------------------------------
18:26:03.822 INFO  FilterMutectCalls - HTSJDK Version: 3.0.5
18:26:03.822 INFO  FilterMutectCalls - Picard Version: 3.0.0
18:26:03.822 INFO  FilterMutectCalls - Built for Spark Version: 3.3.1
18:26:03.822 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:26:03.822 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:26:03.823 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:26:03.823 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:26:03.823 INFO  FilterMutectCalls - Deflater: IntelDeflater
18:26:03.823 INFO  FilterMutectCalls - Inflater: IntelInflater
18:26:03.823 INFO  FilterMutectCalls - GCS max retries/reopens: 20
18:26:03.823 INFO  FilterMutectCalls - Requester pays: disabled
18:26:03.824 INFO  FilterMutectCalls - Initializing engine
18:26:04.085 INFO  FeatureManager - Using codec VCFCodec to read file file:///global/scratch/users/laurenhamm/thesis/aim2/vcfs/GATK/pooled_vcfs/Mutect2/BEL_2014_pool.M2.g.vcf.gz
18:26:04.287 INFO  FilterMutectCalls - Done initializing engine
18:26:04.435 INFO  ProgressMeter - Starting traversal
18:26:04.436 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:26:04.436 INFO  FilterMutectCalls - Starting pass 0 through the variants
18:26:14.458 INFO  ProgressMeter -       Chr_01:1390539              0.2                310000        1856843.4
18:26:24.461 INFO  ProgressMeter -       Chr_01:3294739              0.3                729000        2184269.7
18:26:34.472 INFO  ProgressMeter -       Chr_01:5491190              0.5               1203000        2403196.3
18:26:44.494 INFO  ProgressMeter -       Chr_01:7521491              0.7               1617000        2422048.6
18:26:54.502 INFO  ProgressMeter -      Chr_01:10725017              0.8               2091000        2505942.3
18:27:04.512 INFO  ProgressMeter -        Chr_02:526496              1.0               2619000        2615686.8
18:27:14.516 INFO  ProgressMeter -       Chr_02:2363017              1.2               3028000        2592502.7
18:27:24.544 INFO  ProgressMeter -       Chr_02:4259066              1.3               3429000        2568314.9
18:27:34.548 INFO  ProgressMeter -       Chr_02:6516352              1.5               3895000        2593439.3
18:27:44.552 INFO  ProgressMeter -       Chr_02:9589885              1.7               4438000        2659714.7
18:27:54.562 INFO  ProgressMeter -      Chr_02:14021730              1.8               5042000        2747035.2
18:28:04.599 INFO  ProgressMeter -      Chr_02:16122563              2.0               5474000        2733310.0
18:28:14.600 INFO  ProgressMeter -      Chr_02:18159243              2.2               5902000        2720567.9
18:28:24.608 INFO  ProgressMeter -      Chr_02:20005692              2.3               6314000        2702679.6
18:28:34.615 INFO  ProgressMeter -       Chr_03:1731594              2.5               6769000        2704372.8
18:28:44.616 INFO  ProgressMeter -       Chr_03:4965726              2.7               7319000        2741557.9
18:28:54.620 INFO  ProgressMeter -      Chr_03:11606895              2.8               8242000        2905813.2
18:29:04.619 INFO  ProgressMeter -      Chr_03:15027197              3.0               8864000        2951665.8
18:29:14.623 INFO  ProgressMeter -      Chr_03:18127638              3.2               9412000        2969288.1
18:29:24.632 INFO  ProgressMeter -      Chr_03:20071338              3.3               9805000        2938620.2
18:29:34.637 INFO  ProgressMeter -      Chr_03:22005197              3.5              10220000        2917207.8
18:29:44.648 INFO  ProgressMeter -      Chr_03:23765861              3.7              10610000        2890863.8
18:29:54.677 INFO  ProgressMeter -       Chr_04:1764837              3.8              11012000        2869688.7
18:30:04.694 INFO  ProgressMeter -       Chr_04:3431585              4.0              11393000        2845191.4
18:30:14.713 INFO  ProgressMeter -       Chr_04:4886593              4.2              11735000        2813282.9
18:30:24.714 INFO  ProgressMeter -       Chr_04:6488097              4.3              12077000        2784033.9
18:30:34.732 INFO  ProgressMeter -       Chr_04:8540842              4.5              12465000        2766966.6
18:30:44.735 INFO  ProgressMeter -      Chr_04:11071695              4.7              12875000        2755995.4
18:30:54.750 INFO  ProgressMeter -      Chr_04:15628955              4.8              13389000        2767151.3
18:31:04.773 INFO  ProgressMeter -      Chr_04:17761910              5.0              13778000        2752508.0
18:31:14.796 INFO  ProgressMeter -      Chr_04:20039794              5.2              14217000        2748494.5
18:31:24.804 INFO  ProgressMeter -      Chr_04:21787042              5.3              14596000        2733606.4
18:31:34.824 INFO  ProgressMeter -        Chr_05:765644              5.5              14979000        2720256.2
18:31:44.839 INFO  ProgressMeter -       Chr_05:2436743              5.7              15344000        2704559.0
18:31:54.842 INFO  ProgressMeter -       Chr_05:4239721              5.8              15744000        2695844.2
18:32:04.849 INFO  ProgressMeter -       Chr_05:6232360              6.0              16164000        2690920.4
18:32:14.850 INFO  ProgressMeter -       Chr_05:9651569              6.2              16670000        2700221.9
18:32:24.861 INFO  ProgressMeter -      Chr_05:14352151              6.3              17209000        2714182.1
18:32:34.876 INFO  ProgressMeter -      Chr_05:17368042              6.5              17730000        2724625.4
18:32:44.889 INFO  ProgressMeter -      Chr_05:19691104              6.7              18198000        2726612.1
18:32:54.913 INFO  ProgressMeter -      Chr_05:21576401              6.8              18609000        2720103.7
18:33:04.925 INFO  ProgressMeter -       Chr_06:1574809              7.0              19004000        2711706.4
18:33:14.936 INFO  ProgressMeter -       Chr_06:3452354              7.2              19417000        2706208.4
18:33:24.943 INFO  ProgressMeter -       Chr_06:5120080              7.3              19795000        2696211.4
18:33:34.964 INFO  ProgressMeter -       Chr_06:7054808              7.5              20185000        2688179.2
18:33:44.965 INFO  ProgressMeter -       Chr_06:9812669              7.7              20630000        2687778.6
18:33:54.987 INFO  ProgressMeter -      Chr_06:14258418              7.8              21185000        2701301.2
18:34:04.997 INFO  ProgressMeter -      Chr_06:16608857              8.0              21603000        2697222.6
18:34:15.008 INFO  ProgressMeter -      Chr_06:18724622              8.2              22011000        2692081.9
18:34:25.012 INFO  ProgressMeter -      Chr_06:20209527              8.3              22343000        2678074.9
18:34:35.029 INFO  ProgressMeter -        Chr_07:820877              8.5              22681000        2665253.9
18:34:45.043 INFO  ProgressMeter -       Chr_07:2416804              8.7              23038000        2655136.5
18:34:55.045 INFO  ProgressMeter -       Chr_07:4145179              8.8              23386000        2644438.1
18:35:05.050 INFO  ProgressMeter -       Chr_07:6357468              9.0              23811000        2642661.9
18:35:15.065 INFO  ProgressMeter -       Chr_07:9260726              9.2              24287000        2646464.3
18:35:25.083 INFO  ProgressMeter -      Chr_07:14890342              9.3              24844000        2658785.3
18:35:35.085 INFO  ProgressMeter -      Chr_07:18483080              9.5              25314000        2661601.1
18:35:45.095 INFO  ProgressMeter -         Chr_08:19623              9.7              25793000        2665217.7
18:35:55.117 INFO  ProgressMeter -       Chr_08:1786068              9.8              26188000        2660120.5
18:36:05.148 INFO  ProgressMeter -       Chr_08:3492298             10.0              26559000        2652752.1
18:36:15.153 INFO  ProgressMeter -       Chr_08:5465711             10.2              26937000        2646430.3
18:36:25.173 INFO  ProgressMeter -       Chr_08:7439008             10.3              27308000        2639572.0
18:36:35.192 INFO  ProgressMeter -       Chr_08:9626591             10.5              27679000        2632935.7
18:36:45.220 INFO  ProgressMeter -      Chr_08:15661053             10.7              28315000        2651287.6
18:36:55.224 INFO  ProgressMeter -      Chr_08:17753429             10.8              28728000        2648604.5
18:37:05.238 INFO  ProgressMeter -      Chr_08:19456315             11.0              29089000        2641245.0
18:37:15.265 INFO  ProgressMeter -      Chr_08:21153854             11.2              29455000        2634501.5
18:37:25.275 INFO  ProgressMeter -      Chr_08:23004364             11.3              29839000        2629612.3
18:37:35.297 INFO  ProgressMeter -      Chr_08:25085033             11.5              30245000        2626726.1
18:37:45.311 INFO  ProgressMeter -      Chr_08:26760056             11.7              30601000        2619672.0
18:37:55.336 INFO  ProgressMeter -        Chr_09:996706             11.8              31011000        2617330.1
18:38:05.336 INFO  ProgressMeter -       Chr_09:3088198             12.0              31470000        2619226.0
18:38:15.363 INFO  ProgressMeter -       Chr_09:6049789             12.2              32029000        2629181.8
18:38:25.373 INFO  ProgressMeter -      Chr_09:17117473             12.3              32832000        2658687.6
18:38:35.376 INFO  ProgressMeter -      Chr_09:20110413             12.5              33390000        2667859.8
18:38:45.385 INFO  ProgressMeter -      Chr_09:22155836             12.7              33829000        2667379.8
18:38:55.400 INFO  ProgressMeter -      Chr_09:24122725             12.8              34257000        2666042.3
18:39:05.423 INFO  ProgressMeter -        Chr_10:752399             13.0              34656000        2662477.1
18:39:15.451 INFO  ProgressMeter -       Chr_10:2601252             13.2              35071000        2660202.4
18:39:25.458 INFO  ProgressMeter -       Chr_10:4342361             13.4              35447000        2655136.4
18:39:35.472 INFO  ProgressMeter -       Chr_10:6166656             13.5              35816000        2649648.1
18:39:45.487 INFO  ProgressMeter -       Chr_10:8476442             13.7              36249000        2648973.9
18:39:55.499 INFO  ProgressMeter -      Chr_10:13241422             13.9              36866000        2661603.3
18:40:05.520 INFO  ProgressMeter -      Chr_10:16001442             14.0              37371000        2665916.8
18:40:15.526 INFO  ProgressMeter -      Chr_10:18296227             14.2              37803000        2665029.6
18:40:25.539 INFO  ProgressMeter -      Chr_10:20261280             14.4              38208000        2662263.0
18:40:35.555 INFO  ProgressMeter -      Chr_10:22063860             14.5              38604000        2658931.0
18:40:45.566 INFO  ProgressMeter -       Chr_11:1740195             14.7              39004000        2655956.2
18:40:55.569 INFO  ProgressMeter -       Chr_11:3433124             14.9              39376000        2651186.7
18:41:05.582 INFO  ProgressMeter -       Chr_11:6051065             15.0              39813000        2650824.6
18:41:15.603 INFO  ProgressMeter -       Chr_11:8559968             15.2              40231000        2649196.0
18:41:25.607 INFO  ProgressMeter -      Chr_11:18019739             15.4              40967000        2668364.5
18:41:35.607 INFO  ProgressMeter -      Chr_11:23914367             15.5              41568000        2678433.9
18:41:45.614 INFO  ProgressMeter -      Chr_11:26715275             15.7              42042000        2680176.0
18:41:55.636 INFO  ProgressMeter -      Chr_11:31973834             15.9              42624000        2688648.7
18:42:05.638 INFO  ProgressMeter -        Chr_12:476433             16.0              43060000        2687884.5
18:42:15.640 INFO  ProgressMeter -       Chr_12:2490649             16.2              43474000        2685779.7
18:42:25.650 INFO  ProgressMeter -       Chr_12:4647805             16.4              43920000        2685652.7
18:42:35.652 INFO  ProgressMeter -       Chr_12:7219400             16.5              44388000        2686881.6
18:42:45.665 INFO  ProgressMeter -      Chr_12:16508056             16.7              45464000        2724491.6
18:42:55.673 INFO  ProgressMeter -      Chr_12:18800191             16.9              45923000        2724764.5
18:43:05.681 INFO  ProgressMeter -      Chr_12:20791595             17.0              46344000        2722796.9
18:43:15.691 INFO  ProgressMeter -      Chr_12:22576529             17.2              46723000        2718415.9
18:43:25.708 INFO  ProgressMeter -      Chr_12:24152025             17.4              47076000        2712605.4
18:43:35.783 INFO  ProgressMeter -      Chr_12:25631737             17.5              47418000        2706128.4
18:43:45.808 INFO  ProgressMeter -       Chr_13:1540288             17.7              47794000        2701823.7
18:43:55.817 INFO  ProgressMeter -       Chr_13:3951045             17.9              48222000        2700551.9
18:44:05.825 INFO  ProgressMeter -       Chr_13:6213503             18.0              48635000        2698473.9
18:44:15.830 INFO  ProgressMeter -      Chr_13:19457189             18.2              49266000        2708426.1
18:44:25.860 INFO  ProgressMeter -      Chr_13:22468441             18.4              49740000        2709583.2
18:44:35.863 INFO  ProgressMeter -      Chr_13:24770177             18.5              50200000        2710029.5
18:44:45.868 INFO  ProgressMeter -      Chr_13:26666023             18.7              50612000        2707897.3
18:44:55.887 INFO  ProgressMeter -      Chr_13:28376261             18.9              50992000        2704070.0
18:45:05.900 INFO  ProgressMeter -      Chr_13:30044233             19.0              51371000        2700271.5
18:45:15.915 INFO  ProgressMeter -       Chr_14:1048127             19.2              51772000        2697680.7
18:45:25.930 INFO  ProgressMeter -       Chr_14:2727092             19.4              52140000        2693427.6
18:45:35.941 INFO  ProgressMeter -       Chr_14:4564611             19.5              52525000        2690131.7
18:45:45.968 INFO  ProgressMeter -       Chr_14:6654467             19.7              52919000        2687309.9
18:45:55.993 INFO  ProgressMeter -       Chr_14:8553792             19.9              53303000        2684034.4
18:46:06.006 INFO  ProgressMeter -      Chr_14:10554065             20.0              53710000        2681991.1
18:46:16.031 INFO  ProgressMeter -      Chr_14:15290967             20.2              54199000        2684017.9
18:46:26.041 INFO  ProgressMeter -      Chr_14:17231346             20.4              54580000        2680735.6
18:46:36.069 INFO  ProgressMeter -      Chr_14:18928050             20.5              54917000        2675328.3
18:46:46.073 INFO  ProgressMeter -      Chr_14:20767444             20.7              55274000        2671022.2
18:46:56.080 INFO  ProgressMeter -      Chr_14:22347248             20.9              55615000        2666013.7
18:47:06.089 INFO  ProgressMeter -      Chr_14:23959417             21.0              55975000        2661983.9
18:47:16.109 INFO  ProgressMeter -      Chr_14:25495584             21.2              56325000        2657522.8
18:47:26.127 INFO  ProgressMeter -      Chr_14:27086960             21.4              56675000        2653135.6
18:47:35.884 INFO  FilterMutectCalls - Finished pass 0 through the variants
18:47:36.850 INFO  FilterMutectCalls - Shutting down engine
[December 3, 2024, 6:47:36 PM PST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 21.56 minutes.
Runtime.totalMemory()=3428843520
java.lang.IllegalArgumentException: alpha must be greater than 0 but got NaN
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
    at org.broadinstitute.hellbender.utils.param.ParamUtils.isPositive(ParamUtils.java:165)
    at org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape.<init>(BetaDistributionShape.java:13)
    at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster.getFuzzyBinomial(BinomialCluster.java:43)
    at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster.<init>(BinomialCluster.java:17)
    at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.initializeClusters(SomaticClusteringModel.java:184)
    at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:325)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:153)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:165)
    at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
    at org.broadinstitute.hellbender.Main.main(Main.java:306)

for VariantFiltration/SelectVariants:

Using GATK jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-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 -Xmx4g -jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar VariantFiltration -V BEL_2014_pool.M2.g.vcf.gz -filter QD < 2.0 --filter-name QD2 -filter QUAL < 30.0 --filter-name QUAL30 -filter SOR > 3.0 --filter-name SOR3 -filter FS > 60.0 --filter-name FS60 -filter MQ < 40 --filter-name MQ40 -filter MQRankSum < -12.5 --filter-name MQRankSum-12.5 -filter ReadPosRankSum < 8.0 --filter-name ReadPosRankSum8 -O FilterAnno/BEL_2014_pool.M2.FilterAnno.vcf.gz
12:53:19.002 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:53:19.039 INFO  VariantFiltration - ------------------------------------------------------------
12:53:19.044 INFO  VariantFiltration - The Genome Analysis Toolkit (GATK) v4.4.0.0-43-gd79823f-SNAPSHOT
12:53:19.044 INFO  VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
12:53:19.044 INFO  VariantFiltration - Executing as laurenhamm@n0220.savio2 on Linux v4.18.0-553.5.1.el8_10.x86_64 amd64
12:53:19.044 INFO  VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v22.0.1+8-16
12:53:19.045 INFO  VariantFiltration - Start Date/Time: December 4, 2024, 12:53:18 PM PST
12:53:19.045 INFO  VariantFiltration - ------------------------------------------------------------
12:53:19.045 INFO  VariantFiltration - ------------------------------------------------------------
12:53:19.045 INFO  VariantFiltration - HTSJDK Version: 3.0.5
12:53:19.046 INFO  VariantFiltration - Picard Version: 3.0.0
12:53:19.046 INFO  VariantFiltration - Built for Spark Version: 3.3.1
12:53:19.046 INFO  VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:53:19.046 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:53:19.046 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:53:19.046 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:53:19.046 INFO  VariantFiltration - Deflater: IntelDeflater
12:53:19.047 INFO  VariantFiltration - Inflater: IntelInflater
12:53:19.047 INFO  VariantFiltration - GCS max retries/reopens: 20
12:53:19.047 INFO  VariantFiltration - Requester pays: disabled
12:53:19.047 INFO  VariantFiltration - Initializing engine
12:53:19.189 INFO  FeatureManager - Using codec VCFCodec to read file file:///global/scratch/users/laurenhamm/thesis/aim2/vcfs/GATK/pooled_vcfs/Mutect2/BEL_2014_pool.M2.g.vcf.gz
12:53:19.272 INFO  VariantFiltration - Done initializing engine
12:53:19.323 INFO  ProgressMeter - Starting traversal
12:53:19.323 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
12:53:19.334 WARN  JexlEngine - ![0,2]: 'MQ < 40;' undefined variable MQ
12:53:19.335 WARN  JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
12:53:19.335 WARN  JexlEngine - ![0,2]: 'FS > 60.0;' undefined variable FS
12:53:19.335 WARN  JexlEngine - ![0,14]: 'ReadPosRankSum < 8.0;' undefined variable ReadPosRankSum
12:53:19.335 WARN  JexlEngine - ![0,3]: 'SOR > 3.0;' undefined variable SOR
12:53:19.335 WARN  JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
##the warnings above repeat too much to fully include
03:28:34.185 INFO  ProgressMeter -     IM62v2_mt:522486             75.6              37655643         498181.7
03:28:34.185 INFO  ProgressMeter - Traversal complete. Processed 37655643 total variants in 75.6 minutes.
03:28:34.264 INFO  VariantFiltration - Shutting down engine
[December 6, 2024, 3:28:34 AM PST] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 75.59 minutes.
Runtime.totalMemory()=1105199104
Using GATK jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-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 -Xmx4g -jar /global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar SelectVariants -V FilterAnno/YVO_2015_pool.M2.FilterAnno.vcf.gz -select-type SNP --exclude-filtered -O FilterAnno/YVO_2015_pool.M2.FilterAnnp.pruned.vcf.gz
03:28:38.827 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/global/scratch/users/laurenhamm/thesis/software/gatk/build/libs/gatk-package-4.4.0.0-43-gd79823f-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
03:28:38.866 INFO  SelectVariants - ------------------------------------------------------------
03:28:38.871 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.4.0.0-43-gd79823f-SNAPSHOT
03:28:38.871 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
03:28:38.871 INFO  SelectVariants - Executing as laurenhamm@n0220.savio2 on Linux v4.18.0-553.5.1.el8_10.x86_64 amd64
03:28:38.871 INFO  SelectVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v22.0.1+8-16
03:28:38.871 INFO  SelectVariants - Start Date/Time: December 6, 2024, 3:28:38 AM PST
03:28:38.871 INFO  SelectVariants - ------------------------------------------------------------
03:28:38.872 INFO  SelectVariants - ------------------------------------------------------------
03:28:38.872 INFO  SelectVariants - HTSJDK Version: 3.0.5
03:28:38.872 INFO  SelectVariants - Picard Version: 3.0.0
03:28:38.872 INFO  SelectVariants - Built for Spark Version: 3.3.1
03:28:38.873 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:28:38.873 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:28:38.873 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:28:38.873 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:28:38.873 INFO  SelectVariants - Deflater: IntelDeflater
03:28:38.873 INFO  SelectVariants - Inflater: IntelInflater
03:28:38.874 INFO  SelectVariants - GCS max retries/reopens: 20
03:28:38.874 INFO  SelectVariants - Requester pays: disabled
03:28:38.874 INFO  SelectVariants - Initializing engine
03:28:39.009 INFO  FeatureManager - Using codec VCFCodec to read file file:///global/scratch/users/laurenhamm/thesis/aim2/vcfs/GATK/pooled_vcfs/Mutect2/FilterAnno/YVO_2015_pool.M2.FilterAnno.vcf.gz
03:28:39.069 INFO  SelectVariants - Done initializing engine
03:28:39.101 INFO  ProgressMeter - Starting traversal
03:28:39.102 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
03:30:01.151 INFO  ProgressMeter -             unmapped              1.4                     0              0.0
03:30:01.151 INFO  ProgressMeter - Traversal complete. Processed 0 total variants in 1.4 minutes.
03:30:01.157 INFO  SelectVariants - Shutting down engine
[December 6, 2024, 3:30:01 AM PST] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 1.37 minutes.
Runtime.totalMemory()=1105199104