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The gatk GenotypeGVCFs produced an error: java.lang.IllegalArgumentException: sequenceNames.size() != indices.length

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9 comments

  • Avatar
    Bingdi Liu

    Dear All,

    I've checked the output of CombineGVCFs and individual gVCF(ERC GVCF) again. A lot of missing variants present in individual gVCF(ERC GVCF) are also present in the output of CombineGVCFs. However, the output of GenotypeGVCFs exclude these variants. I didn't know why and how GenotypeGVCFs exclude them. I know there could be a threshold of confidence for genotype calling, but I don't know how the calculation of confidence could be influenced.

    Previously, I have merged 2 samples by CombineGVCFs and the output of CombineGVCFs produced much more(about 10 times) variants than this time(total 11 samples: 10 individual samples and 1 sample merged from previous 10 bam files). Does that mean the sequencing depth and the number of samples could influence the calculation of confidence? 

    It's a bit weird as some articles said the joint calling could help to find more variants than the individual one. Could you help me to figure it out?

    Thank you for your attention.

     

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    Bingdi Liu

    Dear All,

    There are more information. I've checked the log message of CombineGVCFs again and just found it also produced an error: 

    java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator

    at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:107)

    at java.util.Iterator.forEachRemaining(Iterator.java:116)

    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)

    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)

    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)

    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)

    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)

    at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)

    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:163)

    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

    at org.broadinstitute.hellbender.Main.main(Main.java:289)

    In addition, I've found there is a warning during the merging process:

    14:40:49.093 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 1597955.SAMEA3448422.CXOO01000002:15089 the annotation MLEAC=[1, 0] was not a numerical value and was ignored.

    bsub message: Exited with exit code 3.

    I'm not sure whether these errors and warnings have influenced the downstream GenotypeGVCFs or not. Could you help me to figure it out? Thanks again.

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    Bingdi Liu

    I've sorted 2 individual gVCFs with reference_genomes46.fasta by SortVcf and then did CombineGVCFs, but it still produced the same error: java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator.

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    Genevieve Brandt

    Bingdi Liu the error message in CombineGVCFs looks like it caused the job to stop running. Please post your GATK version number, exact command, and complete stack trace.

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    Bingdi Liu

    Dear Genevieve,

    Thank you for your reply and below is the information about CombineGVCFs. The individual final gVCF is from the bam file where individual sample reads mapped to the subset of reference_genomes46.fasta. In addition, the contig order is different from that of reference_genomes46.fasta.

    a)Version: 4.1.8.1

    b)Command:

    gatk CombineGVCFs -R /storage1/fangqiong/Active/bingdi/river_project/reference_genomes46.fasta --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S6/S6_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S11/S11_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S12/S12_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S13/S13_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S18/S18_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S20/S20_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S29/S29_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S30/S30_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S32/S32_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S38/S38_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/mergeS/Smerged_final.g.vcf.gz -O /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/multiVCF/Smult.g.vcf.gz

    c)Log:

    14:40:01.912 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/research/bingdi/miniconda3/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

    Oct 06, 2020 2:40:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

    INFO: Failed to detect whether we are running on Google Compute Engine.

    14:40:03.396 INFO  CombineGVCFs - ------------------------------------------------------------

    14:40:03.397 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.8.1

    14:40:03.397 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/

    14:40:03.399 INFO  CombineGVCFs - Executing as bingdi@node22.engr.wustl.edu on Linux v5.4.15-1.el7.elrepo.x86_64 amd64

    14:40:03.399 INFO  CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11

    14:40:03.400 INFO  CombineGVCFs - Start Date/Time: October 6, 2020 2:40:01 PM CDT

    14:40:03.400 INFO  CombineGVCFs - ------------------------------------------------------------

    14:40:03.400 INFO  CombineGVCFs - ------------------------------------------------------------

    14:40:03.401 INFO  CombineGVCFs - HTSJDK Version: 2.23.0

    14:40:03.402 INFO  CombineGVCFs - Picard Version: 2.22.8

    14:40:03.402 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2

    14:40:03.402 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

    14:40:03.402 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

    14:40:03.402 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

    14:40:03.402 INFO  CombineGVCFs - Deflater: IntelDeflater

    14:40:03.402 INFO  CombineGVCFs - Inflater: IntelInflater

    14:40:03.402 INFO  CombineGVCFs - GCS max retries/reopens: 20

    14:40:03.402 INFO  CombineGVCFs - Requester pays: disabled

    14:40:03.403 INFO  CombineGVCFs - Initializing engine

    14:40:04.281 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S6/S6_final.g.vcf.gz

    14:40:04.594 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S11/S11_final.g.vcf.gz

    14:40:05.007 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S12/S12_final.g.vcf.gz

    14:40:05.521 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S13/S13_final.g.vcf.gz

    14:40:06.050 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S18/S18_final.g.vcf.gz

    14:40:06.580 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S20/S20_final.g.vcf.gz

    14:40:07.034 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S29/S29_final.g.vcf.gz

    14:40:07.510 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S30/S30_final.g.vcf.gz

    14:40:07.992 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S32/S32_final.g.vcf.gz

    14:40:08.446 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S38/S38_final.g.vcf.gz

    14:40:08.936 INFO  FeatureManager - Using codec VCFCodec to read file file:///storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/mergeS/Smerged_final.g.vcf.gz

    14:40:48.566 INFO  CombineGVCFs - Done initializing engine

    14:40:48.706 INFO  ProgressMeter - Starting traversal

    14:40:48.706 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

    14:40:49.093 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 1597955.SAMEA3448422.CXOO01000002:15089 the annotation MLEAC=[1, 0] was not a numerical value and was ignored

    14:40:58.728 INFO  ProgressMeter - 1597955.SAMEA3448422.CXOO01000023:27284              0.2                364000        2183563.3

    14:41:08.904 INFO  ProgressMeter - 1597955.SAMEA3448422.CXOO01000038:13357              0.3                603000        1792953.1

    14:41:19.099 INFO  ProgressMeter - 1597955.SAMEA3448422.CXOO01000055:31758              0.5                827000        1633634.0

    14:41:29.199 INFO  ProgressMeter - 1581557.SAMEA3165955.LN827929:173428              0.7               1042000        1544695.4

    14:41:39.363 INFO  ProgressMeter - 1581557.SAMEA3165955.LN827929:430502              0.8               1268000        1502458.7

    14:41:49.363 INFO  ProgressMeter - 1581557.SAMEA3165955.LN827929:982956              1.0               1492000        1476302.0

    14:41:59.414 INFO  ProgressMeter - 1581557.SAMEA3165955.LN827929:1282980              1.2               1698000        1441263.0

    14:42:09.509 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000001:91966              1.3               1973000        1465389.2

    14:42:19.539 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000002:6273              1.5               2231000        1474001.8

    14:42:29.664 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000003:87100              1.7               2705000        1607901.8

    14:42:39.705 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000005:4702              1.8               2931000        1584609.8

    14:42:49.812 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000005:114450              2.0               3171000        1571266.9

    14:42:59.857 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000006:91223              2.2               3395000        1553396.6

    14:43:10.033 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000008:36295              2.4               3632000        1542163.2

    14:43:20.122 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000010:16488              2.5               3899000        1545209.0

    14:43:30.122 INFO  ProgressMeter - 932044.SAMN02261280.AQUA01000025:267              2.7               4129000        1534972.8

    14:43:40.128 INFO  ProgressMeter - 932039.SAMN02256500.AQYZ01000008:5240              2.9               4359000        1525877.6

    14:43:50.135 INFO  ProgressMeter - 932039.SAMN02256500.AQYZ01000029:1824              3.0               4592000        1518769.6

    14:44:00.209 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000001:68925              3.2               4818000        1509682.3

    14:44:10.220 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000001:200116              3.4               5046000        1502568.3

    14:44:20.317 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:19958              3.5               5279000        1496937.5

    14:44:30.615 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:159755              3.7               5592000        1512100.6

    14:44:40.624 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:302806              3.9               5924000        1532736.2

    14:44:50.714 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:455374              4.0               6255000        1550896.9

    14:45:00.724 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:584228              4.2               6570000        1564291.9

    14:45:10.991 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:729208              4.4               6888000        1575804.7

    14:45:21.031 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000002:824391              4.5               7109000        1566399.6

    14:45:31.031 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000003:96023              4.7               7329000        1557671.5

    14:45:41.036 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000004:2512              4.9               7712000        1582971.6

    14:45:51.168 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000004:102400              5.0               7927000        1572593.8

    14:46:01.272 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000005:7473              5.2               8151000        1564756.7

    14:46:11.272 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000005:110510              5.4               8398000        1562190.9

    14:46:21.272 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000006:51814              5.5               8673000        1564831.4

    14:46:31.279 INFO  ProgressMeter - 1798013.SAMN04313842.MGWH01000006:238080              5.7               9097000        1593383.8

    14:46:41.309 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000007:48480              5.9               9432000        1605064.3

    14:46:51.492 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000018:29687              6.0               9723000        1608139.7

    14:47:01.542 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000028:76780              6.2              10065000        1619829.6

    14:47:11.549 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000031:74157              6.4              10337000        1620117.9

    14:47:21.552 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000034:54145              6.5              10639000        1624990.1

    14:47:31.563 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000043:76502              6.7              11015000        1640609.9

    14:47:41.578 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000045:226564              6.9              11233000        1632493.9

    14:47:51.600 INFO  ProgressMeter - 1100720.SAMN02470021.ALKN01000051:3727              7.0              11524000        1635093.1

    14:48:01.651 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:117964              7.2              11942000        1655063.5

    14:48:11.657 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:299068              7.4              12440000        1685134.5

    14:48:21.662 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:388655              7.5              12669000        1678246.6

    14:48:31.663 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:483517              7.7              12908000        1672967.0

    14:48:41.669 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:574695              7.9              13142000        1667258.7

    14:48:51.682 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:666930              8.0              13370000        1661017.4

    14:49:01.906 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:778093              8.2              13647000        1660282.9

    14:49:12.029 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000001:890981              8.4              13923000        1659792.1

    14:49:22.084 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:78880              8.6              14265000        1667254.3

    14:49:32.129 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:174242              8.7              14493000        1661393.5

    14:49:42.142 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:292766              8.9              14777000        1662151.7

    14:49:52.215 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:377654              9.1              14998000        1655743.4

    14:50:02.267 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:545941              9.2              15460000        1675753.6

    14:50:12.303 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:739144              9.4              15956000        1698717.8

    14:50:22.423 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:824748              9.6              16185000        1692702.4

    14:50:32.454 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000002:907224              9.7              16419000        1687666.7

    14:50:42.461 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000003:120710              9.9              16793000        1697016.9

    14:50:52.467 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000003:212632             10.1              17024000        1691848.5

    14:51:02.481 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000003:295755             10.2              17255000        1686826.7

    14:51:12.642 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000003:375414             10.4              17486000        1681569.8

    14:51:22.701 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000004:61255             10.6              17722000        1677224.4

    14:51:32.775 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000004:146352             10.7              17960000        1673162.0

    14:51:42.853 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000004:222054             10.9              18184000        1667930.4

    14:51:52.881 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000005:12087             11.1              18446000        1666415.7

    14:52:02.881 INFO  ProgressMeter - 1100719.SAMEA3448423.CXOM01000006:13006             11.2              18719000        1665994.2

    14:52:12.891 INFO  ProgressMeter - 932036.SAMN02261283.KB900543:26765             11.4              19220000        1685555.8

    14:52:22.986 INFO  ProgressMeter - 932036.SAMN02261283.KB900550:2923             11.6              19551000        1689652.7

    14:52:33.003 INFO  ProgressMeter - 932036.SAMN02261283.KB900559:1320             11.7              19802000        1687006.7

    14:52:43.173 INFO  ProgressMeter - 932036.SAMN02261283.KB900573:48742             11.9              20058000        1684489.3

    14:52:53.175 INFO  ProgressMeter - 932036.SAMN02261283.KB900595:34321             12.1              20305000        1681689.6

    14:53:03.324 INFO  ProgressMeter - 932036.SAMN02261283.KB900602:42059             12.2              20538000        1677486.6

    14:53:13.526 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:115130             12.4              20771000        1673279.2

    14:53:23.636 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:452190             12.6              20981000        1667560.8

    14:53:33.643 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:881139             12.7              21191000        1662217.4

    14:53:43.948 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:1165136             12.9              21409000        1656994.2

    14:53:54.077 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:1515395             13.1              21603000        1650444.6

    14:54:04.217 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:1825710             13.3              21828000        1646379.4

    14:54:14.333 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:2043167             13.4              22052000        1642386.9

    14:54:24.611 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:2407278             13.6              22267000        1637508.2

    14:54:34.615 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:2703841             13.8              22483000        1633365.2

    14:54:44.626 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:3010623             13.9              22692000        1628805.3

    14:54:54.671 INFO  ProgressMeter - 1678128.SAMN03569611.CP011774:3299144             14.1              22902000        1624359.0

    14:55:04.675 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000001:31520             14.3              23098000        1619113.3

    14:55:14.717 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000007:100248             14.4              23295000        1613987.2

    14:55:24.733 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000014:59494             14.6              23569000        1614300.3

    14:55:34.805 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000021:152675             14.8              23809000        1612203.9

    14:55:44.963 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000023:16187             14.9              24019000        1607988.1

    14:55:54.986 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000030:79026             15.1              24224000        1603778.2

    14:56:04.985 INFO  ProgressMeter - 1797746.SAMN04314158.MGPB01000034:93672             15.3              24428000        1599633.3

    14:56:15.402 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000001:440             15.4              24651000        1596090.1

    14:56:25.526 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000001:110956             15.6              24897000        1594596.9

    14:56:35.530 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000001:230717             15.8              25138000        1593020.7

    14:56:45.536 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000002:132711             15.9              25661000        1609157.9

    14:56:55.585 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000003:43414             16.1              26066000        1617567.8

    14:57:05.612 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000003:263781             16.3              26523000        1629031.8

    14:57:15.760 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000003:374175             16.5              26763000        1626872.4

    14:57:25.866 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000003:497409             16.6              27019000        1625788.1

    14:57:35.890 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000003:630316             16.8              27290000        1625751.5

    14:57:46.046 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000005:96045             17.0              27573000        1626212.4

    14:57:56.094 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000008:59309             17.1              27822000        1624851.1

    14:58:06.230 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000009:68047             17.3              28068000        1623201.8

    14:58:16.256 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000009:174436             17.5              28309000        1621469.9

    14:58:26.294 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000018:92803             17.6              28550000        1619752.5

    14:58:36.419 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000018:190451             17.8              28781000        1617375.0

    14:58:46.585 INFO  ProgressMeter - 1743157.SAMN04074796.LOJJ01000018:294314             18.0              29013000        1615033.5

    14:58:56.598 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000001:35756             18.1              29234000        1612357.3

    14:59:06.614 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000001:152741             18.3              29455000        1609727.0

    14:59:16.777 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000001:349569             18.5              29755000        1611206.0

    14:59:26.784 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000001:531788             18.6              30118000        1616265.3

    14:59:36.978 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000003:62040             18.8              30399000        1616606.9

    14:59:46.978 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000005:53140             19.0              30615000        1613788.9

    14:59:57.017 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000005:154654             19.1              30831000        1610968.0

    15:00:07.023 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000007:20670             19.3              31083000        1610103.8

    15:00:17.035 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000022:97736             19.5              31427000        1613972.3

    15:00:27.038 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000035:23188             19.6              31664000        1612339.0

    15:00:37.094 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000035:141455             19.8              31871000        1609146.7

    15:00:47.109 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000035:253986             20.0              32093000        1606813.8

    15:00:57.169 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000035:397438             20.1              32398000        1608582.3

    15:01:07.257 INFO  ProgressMeter - 1743159.SAMN03400177.LOJI01000040:188102             20.3              32753000        1612745.2

    15:01:17.392 INFO  ProgressMeter - 1835254.SAMN02708862.CP007501:216089             20.5              33191000        1620829.7

    15:01:27.406 INFO  ProgressMeter - 1835254.SAMN02708862.CP007501:559169             20.6              33511000        1623226.6

    15:01:37.519 INFO  ProgressMeter - 1835254.SAMN02708862.CP007501:885845             20.8              33794000        1623679.8

    15:01:47.520 INFO  ProgressMeter - 1835254.SAMN02708862.CP007501:1246395             21.0              34157000        1628080.8

    15:01:57.521 INFO  ProgressMeter - 1835254.SAMN02708862.CP007501:1804568             21.1              34792000        1645276.3

    15:02:07.525 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:171044             21.3              35306000        1656521.7

    15:02:17.529 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:317196             21.5              35586000        1656698.8

    15:02:27.665 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:499129             21.6              35824000        1654764.7

    15:02:37.738 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:632413             21.8              36069000        1653260.9

    15:02:47.777 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:773894             22.0              36310000        1651642.0

    15:02:57.849 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:909814             22.2              36576000        1651132.6

    15:03:07.954 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:1085835             22.3              36871000        1651890.8

    15:03:17.960 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:1358934             22.5              37308000        1659073.5

    15:03:28.053 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:1660957             22.7              37796000        1668296.1

    15:03:38.180 INFO  ProgressMeter - 543913.SAMN02641529.CP004348:1967258             22.8              38260000        1676288.5

    15:03:48.287 INFO  ProgressMeter - 1801989.SAMN04313895.MHZG01000001:685981             23.0              38692000        1682796.2

    15:03:58.383 INFO  ProgressMeter - 1801989.SAMN04313895.MHZG01000011:104665             23.2              39127000        1689350.9

    15:04:08.394 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:116046             23.3              39612000        1698058.6

    15:04:18.408 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:315534             23.5              40154000        1709065.1

    15:04:28.412 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:496485             23.7              40614000        1716464.1

    15:04:38.523 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:674158             23.8              41052000        1722704.9

    15:04:48.626 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:854121             24.0              41538000        1730869.0

    15:04:58.635 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1042811             24.2              42003000        1738163.1

    15:05:08.645 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1206124             24.3              42474000        1745602.5

    15:05:18.663 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1383856             24.5              42974000        1754114.8

    15:05:28.693 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1537497             24.7              43404000        1759660.9

    15:05:38.693 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1706991             24.8              43869000        1766574.9

    15:05:48.696 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:1852586             25.0              44301000        1772074.3

    15:05:58.700 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2013795             25.2              44772000        1779050.5

    15:06:08.772 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2187995             25.3              45242000        1785813.2

    15:06:18.777 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2373344             25.5              45793000        1795742.9

    15:06:28.781 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2570717             25.7              46317000        1804492.8

    15:06:38.883 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2713071             25.8              46717000        1808215.7

    15:06:48.887 INFO  ProgressMeter - 1678129.SAMN03569612.CP011834:2859607             26.0              47135000        1812697.5

    15:06:58.903 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000001:314967             26.2              47656000        1821041.9

    15:07:08.921 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000001:589963             26.3              47991000        1822217.0

    15:07:19.003 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000001:855083             26.5              48352000        1824286.0

    15:07:29.009 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000002:116170             26.7              48777000        1828812.9

    15:07:39.021 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000002:446115             26.8              49200000        1833203.3

    15:07:49.146 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000003:89982             27.0              49498000        1832783.0

    15:07:59.196 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000003:273411             27.2              49733000        1830133.7

    15:08:09.277 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000003:459050             27.3              49956000        1827043.6

    15:08:19.280 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000004:102779             27.5              50186000        1824331.8

    15:08:29.297 INFO  ProgressMeter - 1100721.SAMEA3719354.FBYA01000005:162088             27.7              50629000        1829333.5

    15:08:39.307 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000001:148968             27.8              51120000        1836006.9

    15:08:49.334 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000001:531440             28.0              51701000        1845795.2

    15:08:59.334 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:313445             28.2              52282000        1855497.0

    15:09:09.338 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:566794             28.3              52764000        1861587.6

    15:09:19.338 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:844565             28.5              53286000        1869014.2

    15:09:29.342 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:1184490             28.7              53871000        1878547.1

    15:09:39.348 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:1514689             28.8              54402000        1886095.4

    15:09:49.385 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:1716145             29.0              54750000        1887215.2

    15:09:59.479 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:2003342             29.2              55226000        1892647.4

    15:10:09.490 INFO  ProgressMeter - 1100705.SAMEA3448420.CXOP01000002:2307171             29.3              55787000        1901003.3

    15:10:19.498 INFO  ProgressMeter - 529884.SAMN02848463.CP007490:225677             29.5              56265000        1906455.5

    15:10:29.504 INFO  ProgressMeter - 529884.SAMN02848463.CP007490:528196             29.7              56765000        1912589.9

    15:10:39.537 INFO  ProgressMeter - 529884.SAMN02848463.CP007490:696254             29.8              57075000        1912261.0

    15:10:49.549 INFO  ProgressMeter - 529884.SAMN02848463.CP007490:961115             30.0              57536000        1916989.1

    15:10:59.636 INFO  ProgressMeter - 529884.SAMN02848463.CP007490:1216999             30.2              57990000        1921353.4

    15:11:09.642 INFO  ProgressMeter - 1293045.SAMN03801504.LFYT01000007:533011             30.3              58376000        1923515.4

    15:11:19.644 INFO  ProgressMeter - 1293045.SAMN03801504.LFYT01000006:338668             30.5              58673000        1922739.3

    15:11:29.733 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000001:113660             30.7              59054000        1924619.6

    15:11:39.746 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000001:466659             30.9              59625000        1932718.2

    15:11:49.757 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000002:357819             31.0              60244000        1942277.2

    15:11:59.904 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000003:71735             31.2              60657000        1944987.6

    15:12:09.946 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000003:190879             31.4              60929000        1943280.5

    15:12:20.037 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000004:7372             31.5              61426000        1948680.0

    15:12:30.102 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000004:160241             31.7              61668000        1946000.2

    15:12:40.136 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000005:46813             31.9              61903000        1943161.4

    15:12:50.230 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000005:175570             32.0              62156000        1940853.7

    15:13:00.354 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000005:309172             32.2              62382000        1937701.3

    15:13:10.354 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000006:183534             32.4              62596000        1934334.5

    15:13:20.407 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000008:12377             32.5              62851000        1932210.3

    15:13:30.442 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000008:127063             32.7              63092000        1929698.3

    15:13:40.507 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000009:139991             32.9              63366000        1928185.7

    15:13:50.565 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000011:19948             33.0              63624000        1926210.0

    15:14:00.843 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000012:32782             33.2              63888000        1924223.4

    15:14:10.970 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000013:18235             33.4              64143000        1922132.4

    15:14:20.981 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000014:26833             33.5              64399000        1920203.0

    15:14:31.152 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000015:51253             33.7              64647000        1917903.6

    15:14:41.205 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000016:83257             33.9              64885000        1915443.2

    15:14:51.212 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000018:44654             34.0              65137000        1913461.4

    15:15:01.329 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000020:22311             34.2              65384000        1911251.2

    15:15:11.602 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000021:51629             34.4              65628000        1908829.3

    15:15:21.661 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000028:6938             34.5              66171000        1915283.4

    15:15:31.669 INFO  ProgressMeter - 1100700.SAMEA3448421.CXON01000037:3150             34.7              66617000        1918929.1

    15:15:41.694 INFO  ProgressMeter - 938709.SAMN02440794.AUSH02000017:139792             34.9              66876000        1917161.7

    15:15:51.716 INFO  ProgressMeter - 938709.SAMN02440794.AUSH02000059:14172             35.0              67163000        1916213.6

    15:16:01.970 INFO  ProgressMeter - 938624.SAMN02256512.AQPD01000002:38145             35.2              67439000        1914752.0

    15:16:12.101 INFO  ProgressMeter - 938624.SAMN02256512.AQPD01000006:17832             35.4              67711000        1913303.1

    15:16:22.151 INFO  ProgressMeter - 938624.SAMN02256512.AQPD01000016:10315             35.6              68013000        1912783.4

    15:16:32.273 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000001:76686             35.7              68324000        1912455.4

    15:16:42.328 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000003:180482             35.9              68591000        1910965.9

    15:16:52.331 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000013:111449             36.1              69076000        1915579.8

    15:17:02.347 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000027:20074             36.2              69327000        1913681.4

    15:17:12.456 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000034:4770             36.4              69569000        1911471.7

    15:17:22.463 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000034:375885             36.6              69811000        1909371.1

    15:17:32.510 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000036:130589             36.7              70057000        1907364.8

    15:17:42.636 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000040:237785             36.9              70301000        1905252.7

    15:17:52.638 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000046:33312             37.1              70541000        1903159.8

    15:18:02.775 INFO  ProgressMeter - 1802014.SAMN04315469.MHZT01000048:137337             37.2              70802000        1901533.9

    15:18:10.892 INFO  CombineGVCFs - Shutting down engine

    [October 6, 2020 3:18:11 PM CDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 38.16 minutes.

    Runtime.totalMemory()=1509425152

    java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator

            at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:107)

            at java.util.Iterator.forEachRemaining(Iterator.java:116)

            at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

            at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)

            at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)

            at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)

            at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)

            at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

            at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)

            at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)

            at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:163)

            at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

            at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

            at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

            at org.broadinstitute.hellbender.Main.main(Main.java:289)

    Using GATK jar /home/research/bingdi/miniconda3/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-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/research/bingdi/miniconda3/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar CombineGVCFs -R /storage1/fangqiong/Active/bingdi/river_project/reference_genomes46.fasta --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S6/S6_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S11/S11_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S12/S12_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S13/S13_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S18/S18_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S20/S20_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S29/S29_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S30/S30_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S32/S32_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/S38/S38_final.g.vcf.gz --variant /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/mergeS/Smerged_final.g.vcf.gz -O /storage1/fangqiong/Active/bingdi/river_project/specific_map/specific_alig_result/multiVCF/Smult.g.vcf.gz

     

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    Genevieve Brandt

    Bingdi Liu the VCFs are not sorted. Please see this similar forum post for more information: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057988172-CreateSomaticPanelOfNormals-fails-

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    Bingdi Liu

    I've sorted two VCFs and did CombineGVCFs. It still produced the same problem. I'm wondering whether the inconsistence of reference genome set could cause that problem, as the reference genome set for individual sample is only the different subset of the reference genome set used in CombineGVCFs and their order of contig is different. 

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    Genevieve Brandt

    Hi Bingdi Liu, could you clarify what you mean about using inconsistent references?

    • How many samples were in each VCF before CombineGVCFs?
    • Which references are those samples?
    • Did you use a different reference during CombineGVCFs and now GenotypeGVCFs?
    • Did you sort the VCF after CombineGVCFs?

    It is important to keep your reference consistent for all steps of GATK and this inconsistency will cause issues.

    Please see our documentation on references for more background information: https://gatk.broadinstitute.org/hc/en-us/articles/360035891071-Reference-genome

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    Bingdi Liu

    Dear Genevieve,

    Thank you for your advice and we used different genome set before, since we think the subset of the same genome set would also work. However, it turned wrong so that we use the same new reference genome at all steps now. It works well.

     

    Thanks again.

    Cheers,

    Bingdi Liu

     

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