Somatic Variant Calling for a non-model species not finding any variants
REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
GATK version used: 3.0.1
Exact command used:
/Users/igliving/gatk/gatk Mutect2 \
-R GCF_009762305.2_mZalCal1.pri.v2_genomic.fna \
-I CSL10273T_marked_duplicates.bam \
-I CSL10273N_marked_duplicates.bam \
-normal CSL10273N \
-O somatic.vcf.gz
Entire program log:
Using GATK jar /Users/igliving/gatk/build/libs/gatk-package-4.3.0.0-12-g84ade40-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 -jar /Users/igliving/gatk/build/libs/gatk-package-4.3.0.0-12-g84ade40-SNAPSHOT-local.jar Mutect2 -R GCF_009762305.2_mZalCal1.pri.v2_genomic.fna -I CSL10273T_marked_duplicates.bam -I CSL10273N_marked_duplicates.bam -normal CSL10273N -O somatic.vcf.gz
13:57:48.697 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/igliving/gatk/build/libs/gatk-package-4.3.0.0-12-g84ade40-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
13:57:49.151 INFO Mutect2
13:57:49.155 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.3.0.0-12-
13:57:49.155 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_92-b15
13:57:49.155 INFO Mutect2 - HTSJDK Version: 3.0.1
13:57:49.155 INFO Mutect2 - Picard Version: 2.27.5
13:57:49.155 INFO Mutect2 - Built for Spark Version: 2.4.5
13:57:49.156 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:57:49.156 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:57:49.156 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:57:49.156 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:57:49.156 INFO Mutect2 - Deflater: IntelDeflater
13:57:49.156 INFO Mutect2 - Inflater: IntelInflater
13:57:49.156 INFO Mutect2 - GCS max retries/reopens: 20
13:57:49.156 INFO Mutect2 - Requester pays: disabled
13:57:49.156 INFO Mutect2 - Initializing engine
13:57:49.586 INFO Mutect2 - Done initializing engine
13:57:49.620 INFO NativeLibraryLoader - Loading libgkl_utils.dylib from jar:file:/Users/igliving/gatk/build/libs/gatk-package-4.3.0.0-12-g84ade40-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.dylib
13:57:49.668 WARN NativeLibraryLoader - Unable to find native library: native/libgkl_pairhmm_omp.dylib
13:57:49.668 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
13:57:49.668 INFO NativeLibraryLoader - Loading libgkl_pairhmm.dylib from jar:file:/Users/igliving/gatk/build/libs/gatk-package-4.3.0.0-12-g84ade40-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_pairhmm.dylib
13:57:49.754 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
13:57:49.754 WARN IntelPairHmm - Ignoring request for 4 threads; not using OpenMP implementation
13:57:49.754 INFO PairHMM - Using the AVX-accelerated native PairHMM implementation
13:57:49.791 INFO ProgressMeter - Starting traversal
13:57:49.791 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
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16:59:53.944 INFO ProgressMeter - NC_045602.1:13126971 182.1 5643530 30996.6
17:00:03.954 INFO ProgressMeter - NC_045602.1:14084207 182.2 5648100 30993.3
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17:01:56.158 INFO ProgressMeter - NC_045602.1:22535253 184.1 5688700 30899.0
17:02:06.165 INFO ProgressMeter - NC_045602.1:22895261 184.3 5690540 30881.0
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17:02:36.235 INFO ProgressMeter - NC_045602.1:25406161 184.8 5702510 30862.1
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17:03:16.873 INFO ProgressMeter - NC_045602.1:27796789 185.5 5713990 30811.3
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17:39:04.180 INFO ProgressMeter - NC_045603.1:69555377 221.2 6564040 29669.3
17:39:14.199 INFO ProgressMeter - NC_045603.1:71150547 221.4 6570830 29677.6
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17:40:04.612 INFO ProgressMeter - NC_045603.1:78823624 222.2 6603980 29714.6
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17:40:24.629 INFO ProgressMeter - NC_045603.1:81680657 222.6 6616410 29725.9
17:40:35.850 INFO ProgressMeter - NC_045603.1:83787759 222.8 6625420 29741.4
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17:41:36.991 INFO ProgressMeter - NC_045603.1:91493310 223.8 6657850 29750.9
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17:42:28.900 INFO ProgressMeter - NC_045603.1:97433551 224.7 6684470 29754.8
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17:42:50.893 INFO ProgressMeter - NC_045603.1:98121979 225.0 6687800 29721.1
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18:35:10.688 INFO ProgressMeter - NC_045605.1:103418775 277.3 7885330 28431.1
18:35:20.728 INFO ProgressMeter - NC_045605.1:103936391 277.5 7887970 28423.5
18:35:31.013 INFO ProgressMeter - NC_045605.1:104359894 277.7 7889980 28413.2
18:35:41.069 INFO ProgressMeter - NC_045605.1:104910733 277.9 7892670 28405.8
18:35:51.141 INFO ProgressMeter - NC_045605.1:105498503 278.0 7895600 28399.1
18:36:01.173 INFO ProgressMeter - NC_045605.1:105829605 278.2 7897300 28388.2
18:36:11.185 INFO ProgressMeter - NC_045605.1:106060158 278.4 7898470 28375.4
18:36:21.192 INFO ProgressMeter - NC_045605.1:106574764 278.5 7901040 28367.6
18:36:31.395 INFO ProgressMeter - NC_045605.1:106999406 278.7 7903210 28358.1
18:36:41.409 INFO ProgressMeter - NC_045605.1:107482337 278.9 7905570 28349.6
18:36:51.821 INFO ProgressMeter - NC_045605.1:108132825 279.0 7908740 28343.3
18:37:01.869 INFO ProgressMeter - NC_045605.1:108577336 279.2 7910950 28334.2
18:37:12.128 INFO ProgressMeter - NC_045605.1:109160107 279.4 7913820 28327.1
18:37:22.134 INFO ProgressMeter - NC_045605.1:110051210 279.5 7918240 28326.1
18:37:32.231 INFO ProgressMeter - NC_045605.1:110716126 279.7 7921540 28320.8
18:37:42.247 INFO ProgressMeter - NC_045605.1:111604390 279.9 7925990 28319.8
18:37:52.277 INFO ProgressMeter - NC_045605.1:112142880 280.0 7928780 28312.9
18:38:02.321 INFO ProgressMeter - NC_045605.1:112269374 280.2 7929380 28298.1
18:38:14.011 INFO ProgressMeter - NC_045605.1:112384410 280.4 7929870 28280.2
18:38:24.017 INFO ProgressMeter - NC_045605.1:112744660 280.6 7931750 28270.1
18:38:34.036 INFO ProgressMeter - NC_045605.1:113354805 280.7 7934940 28264.6
18:38:44.088 INFO ProgressMeter - NC_045606.1:772823 280.9 7939410 28263.7
18:38:54.096 INFO ProgressMeter - NC_045606.1:2389002 281.1 7946380 28271.7
18:39:04.134 INFO ProgressMeter - NC_045606.1:4657847 281.2 7955610 28287.7
18:39:14.362 INFO ProgressMeter - NC_045606.1:8118981 281.4 7969160 28318.7
18:39:24.366 INFO ProgressMeter - NC_045606.1:10275804 281.6 7977780 28332.6
18:39:34.405 INFO ProgressMeter - NC_045606.1:13600850 281.7 7990850 28362.1
18:39:45.012 INFO ProgressMeter - NC_045606.1:15116249 281.9 7996870 28365.7
18:39:55.015 INFO ProgressMeter - NC_045606.1:16216936 282.1 8001330 28364.8
18:40:05.019 INFO ProgressMeter - NC_045606.1:18325449 282.3 8009960 28378.6
18:40:15.021 INFO ProgressMeter - NC_045606.1:20517327 282.4 8018680 28392.7
18:40:25.065 INFO ProgressMeter - NC_045606.1:22561622 282.6 8026890 28404.9
18:40:35.066 INFO ProgressMeter - NC_045606.1:25992059 282.8 8040110 28434.9
18:40:45.092 INFO ProgressMeter - NC_045606.1:29389839 282.9 8053120 28464.1
18:40:55.405 INFO ProgressMeter - NC_045606.1:31830128 283.1 8062800 28481.0
18:41:05.418 INFO ProgressMeter - NC_045606.1:34890438 283.3 8074700 28506.3
18:41:15.423 INFO ProgressMeter - NC_045606.1:37155619 283.4 8083650 28521.1
18:41:25.434 INFO ProgressMeter - NC_045606.1:39581601 283.6 8093190 28537.9
18:41:35.442 INFO ProgressMeter - NC_045606.1:43099570 283.8 8106730 28568.9
18:41:45.492 INFO ProgressMeter - NC_045606.1:46373983 283.9 8119450 28596.8
18:41:55.604 INFO ProgressMeter - NC_045606.1:49718399 284.1 8132400 28625.4
18:42:05.790 INFO ProgressMeter - NC_045606.1:52954578 284.3 8144950 28652.5
18:42:15.794 INFO ProgressMeter - NC_045606.1:54976961 284.4 8153130 28664.5
18:42:25.804 INFO ProgressMeter - NC_045606.1:57459649 284.6 8163090 28682.7
18:42:35.834 INFO ProgressMeter - NC_045606.1:59423243 284.8 8171050 28693.8
18:42:45.859 INFO ProgressMeter - NC_045606.1:61688921 284.9 8180190 28709.0
18:42:55.865 INFO ProgressMeter - NC_045606.1:64039715 285.1 8189630 28725.3
18:43:05.876 INFO ProgressMeter - NC_045606.1:66308565 285.3 8198660 28740.2
18:43:15.887 INFO ProgressMeter - NC_045606.1:69668598 285.4 8211600 28768.7
18:43:25.889 INFO ProgressMeter - NC_045606.1:73184983 285.6 8225080 28799.1
18:43:35.889 INFO ProgressMeter - NC_045606.1:75994473 285.8 8236040 28820.7
18:43:45.897 INFO ProgressMeter - NC_045606.1:79221902 285.9 8248650 28848.0
18:43:55.904 INFO ProgressMeter - NC_045606.1:82632913 286.1 8261730 28876.9
18:44:05.920 INFO ProgressMeter - NC_045606.1:83917844 286.3 8267170 28879.0
18:44:15.936 INFO ProgressMeter - NC_045606.1:85793674 286.4 19:19:36.312 INFO ProgressMeter - NC_045608.1:78963928 321.8 9163920 28479.2
19:19:46.342 INFO ProgressMeter - NC_045608.1:79909954 321.9 9168370 28478.3
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19:20:36.493 INFO ProgressMeter - NC_045608.1:85400916 322.8 9193390 28482.1
19:20:46.522 INFO ProgressMeter - NC_045608.1:86613962 322.9 9198920 28484.4
19:20:56.621 INFO ProgressMeter - NC_045608.1:88229751 323.1 9206100 28491.8
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19:22:06.371 INFO ProgressMeter - NC_045608.1:93322267 324.3 9230240 28464.1
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19:22:31.121 INFO ProgressMeter - NC_045608.1:93397601 324.7 9230720 28429.4
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19:22:53.398 INFO ProgressMeter - NC_045608.1:93437013 325.1 9230970 28397.7
19:23:15.763 INFO ProgressMeter - NC_045608.1:93440016 325.4 9231000 28365.3
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19:23:56.759 INFO ProgressMeter - NC_045609.1:2389388 326.1 9245600 28350.6
19:24:06.766 INFO ProgressMeter - NC_045609.1:3956693 326.3 9252420 28357.0
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19:25:26.943 INFO ProgressMeter - NC_045609.1:15056557 327.6 9301720 28391.9
20:19:54.038 INFO ProgressMeter - NW_023365532.1:8858 382.1 10750590 28137.7
20:20:04.634 INFO ProgressMeter - NW_023365532.1:23977 382.2 10750730 28125.1
20:20:16.505 INFO ProgressMeter - NW_023365532.1:29870 382.4 10750780 28110.6
20:20:28.809 INFO ProgressMeter - NW_023365532.1:49742 382.7 10750940 28096.0
20:20:39.499 INFO ProgressMeter - NW_023365532.1:68809 382.8 10751090 28083.3
20:20:49.790 INFO ProgressMeter - NW_023365532.1:73443 383.0 10751120 28070.8
20:21:05.314 INFO ProgressMeter - NW_023365532.1:83895 383.3 10751200 28052.1
20:21:15.375 INFO ProgressMeter - NW_023365532.1:116646 383.4 10751420 28040.4
20:21:25.471 INFO ProgressMeter - NW_023365534.1:43451 383.6 10752340 28030.5
20:21:35.802 INFO ProgressMeter - NW_023365534.1:177776 383.8 10752980 28019.6
20:21:45.932 INFO ProgressMeter - NW_023365534.1:215030 383.9 10753200 28007.8
20:21:56.518 INFO ProgressMeter - NW_023365534.1:277885 384.1 10753540 27995.820:24:29.034 INFO Mutect2 - 3457518 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
693240 read(s) filtered by: NotSecondaryAlignmentReadFilter
13554452 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
17705210 total reads filtered
20:24:29.034 INFO ProgressMeter - NC_008416.1:15402 386.7 10758149 27823.7
20:24:29.034 INFO ProgressMeter - Traversal complete. Processed 10758149 total regions in 386.7 minutes.
20:24:29.271 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.171574091
20:24:29.272 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 3895.1621807740003
20:24:29.272 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 9352.70 sec
20:24:29.273 INFO Mutect2 - Shutting down engine org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 386.68 minutes.
Runtime.totalMemory()=1273495552
Tool returned:
SUCCESS
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