java.io.IOException: Transport endpoint is not connected

[TYU1201]

Dear developers,
At present, I am using GATK's CombineGVCFs module in AWS platform to merge gvcf of 30 samples respectively according to different chromosomes. This species has 10 chromosomes, so a total of 10 CombineGVCFs tasks are carried out in parallel (10 EC2 virtual machines are opened respectively). The input gvcf file is stored in S3 and mounted to the EC2 VM. In this process, java.io.IOException occurs after some samples are analyzed: The Transport endpoint is not connected, but the merged gvcf file and its index are still produced. I did not find any feedback about GATK relation on the Internet, so I would like to know the reason for the error and why some staining machines reported errors. Some will not report errors, in addition, will the gvcf file generated after the "Transport endpoint is not connected" prompt be used? At present, I have tried gatk4.5, 4.4, 4.2 and other versions, and this has happened.

Paste the run log as follows:

06:26:14.775 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
06:26:14.867 INFO  CombineGVCFs - ------------------------------------------------------------
06:26:14.869 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.5.0.0
06:26:14.869 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
06:26:14.869 INFO  CombineGVCFs - Executing as root@ip-10-1-156-254.cn-northwest-1.compute.internal on Linux v4.14.334-252.552.amzn2.x86_64 amd64
06:26:14.869 INFO  CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
06:26:14.869 INFO  CombineGVCFs - Start Date/Time: March 13, 2024 at 6:26:14 AM GMT
06:26:14.869 INFO  CombineGVCFs - ------------------------------------------------------------
06:26:14.869 INFO  CombineGVCFs - ------------------------------------------------------------
06:26:14.870 INFO  CombineGVCFs - HTSJDK Version: 4.1.0
06:26:14.870 INFO  CombineGVCFs - Picard Version: 3.1.1
06:26:14.870 INFO  CombineGVCFs - Built for Spark Version: 3.5.0
06:26:14.870 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
06:26:14.870 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
06:26:14.871 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
06:26:14.871 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
06:26:14.871 INFO  CombineGVCFs - Deflater: IntelDeflater
06:26:14.871 INFO  CombineGVCFs - Inflater: IntelInflater
06:26:14.871 INFO  CombineGVCFs - GCS max retries/reopens: 20
06:26:14.871 INFO  CombineGVCFs - Requester pays: disabled
06:26:14.871 INFO  CombineGVCFs - Initializing engine
06:26:14.993 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR004755/CRR004755.g.vcf.gz
06:26:15.095 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR004757/CRR004757.g.vcf.gz
06:26:15.172 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107621/CRR107621.g.vcf.gz
06:26:15.247 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107651/CRR107651.g.vcf.gz
06:26:15.321 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107656/CRR107656.g.vcf.gz
06:26:15.390 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107664/CRR107664.g.vcf.gz
06:26:15.452 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107668/CRR107668.g.vcf.gz
06:26:15.545 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107683/CRR107683.g.vcf.gz
06:26:15.753 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107728/CRR107728.g.vcf.gz
06:26:15.970 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107757/CRR107757.g.vcf.gz
06:26:16.163 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107766/CRR107766.g.vcf.gz
06:26:16.401 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107789/CRR107789.g.vcf.gz
06:26:16.590 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107791/CRR107791.g.vcf.gz
06:26:16.781 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107811/CRR107811.g.vcf.gz
06:26:16.980 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107814/CRR107814.g.vcf.gz
06:26:17.118 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107815/CRR107815.g.vcf.gz
06:26:17.364 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107902/CRR107902.g.vcf.gz
06:26:17.576 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR107983/CRR107983.g.vcf.gz
06:26:17.748 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108021/CRR108021.g.vcf.gz
06:26:17.937 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108215/CRR108215.g.vcf.gz
06:26:18.116 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108219/CRR108219.g.vcf.gz
06:26:18.294 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108221/CRR108221.g.vcf.gz
06:26:18.466 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108245/CRR108245.g.vcf.gz
06:26:18.635 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108249/CRR108249.g.vcf.gz
06:26:18.809 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108331/CRR108331.g.vcf.gz
06:26:18.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108338/CRR108338.g.vcf.gz
06:26:19.195 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108346/CRR108346.g.vcf.gz
06:26:19.345 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108354/CRR108354.g.vcf.gz
06:26:19.541 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108374/CRR108374.g.vcf.gz
06:26:19.706 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108494/CRR108494.g.vcf.gz
06:26:19.874 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108508/CRR108508.g.vcf.gz
06:26:20.052 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108528/CRR108528.g.vcf.gz
06:26:20.221 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108547/CRR108547.g.vcf.gz
06:26:20.417 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/OutData/proj1/CRR108592/CRR108592.g.vcf.gz
06:26:22.363 INFO  IntervalArgumentCollection - Processing 51272880 bp from intervals
06:26:22.388 INFO  CombineGVCFs - Done initializing engine
06:26:22.401 INFO  ProgressMeter - Starting traversal
06:26:22.401 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
06:26:24.884 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location NC_038255.2:36 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
06:26:32.408 INFO  ProgressMeter -   NC_038255.2:132104              0.2                702000        4209474.3
06:26:42.411 INFO  ProgressMeter -   NC_038255.2:329020              0.3               1725000        5172413.8
06:26:52.415 INFO  ProgressMeter -   NC_038255.2:548109              0.5               2781000        5559405.6
06:27:02.421 INFO  ProgressMeter -   NC_038255.2:735845              0.7               3727000        5587706.1
06:27:12.426 INFO  ProgressMeter -   NC_038255.2:934042              0.8               4757000        5705547.2
06:27:22.431 INFO  ProgressMeter -  NC_038255.2:1124882              1.0               5747000        5744127.9
06:27:32.437 INFO  ProgressMeter -  NC_038255.2:1314436              1.2               6761000        5792164.0
06:27:42.439 INFO  ProgressMeter -  NC_038255.2:1509338              1.3               7653000        5737024.9
06:27:52.446 INFO  ProgressMeter -  NC_038255.2:1709717              1.5               8654000        5766514.1
06:28:02.450 INFO  ProgressMeter -  NC_038255.2:1926291              1.7               9680000        5805155.5
06:28:12.454 INFO  ProgressMeter -  NC_038255.2:2116394              1.8              10674000        5819377.9
06:28:22.458 INFO  ProgressMeter -  NC_038255.2:2306110              2.0              11632000        5813238.7
06:28:32.462 INFO  ProgressMeter -  NC_038255.2:2495782              2.2              12655000        5838029.8
06:28:42.462 INFO  ProgressMeter -  NC_038255.2:2711494              2.3              13674000        5857733.4
06:28:52.469 INFO  ProgressMeter -  NC_038255.2:2908395              2.5              14688000        5872537.8
06:29:02.476 INFO  ProgressMeter -  NC_038255.2:3098143              2.7              15686000        5879530.7
06:29:12.482 INFO  ProgressMeter -  NC_038255.2:3293265              2.8              16712000        5895543.9
06:29:22.486 INFO  ProgressMeter -  NC_038255.2:3490077              3.0              17700000        5897215.2
06:29:32.487 INFO  ProgressMeter -  NC_038255.2:3677366              3.2              18691000        5899750.6
06:29:42.495 INFO  ProgressMeter -  NC_038255.2:3868790              3.3              19671000        5898527.7
06:29:52.504 INFO  ProgressMeter -  NC_038255.2:4068715              3.5              20688000        5907959.4
06:30:02.505 INFO  ProgressMeter -  NC_038255.2:4262962              3.7              21680000        5909933.5
06:30:12.509 INFO  ProgressMeter -  NC_038255.2:4455557              3.8              22679000        5913484.1
06:30:22.510 INFO  ProgressMeter -  NC_038255.2:4654014              4.0              23713000        5925558.8
06:30:32.514 INFO  ProgressMeter -  NC_038255.2:4849390              4.2              24744000        5935877.0
06:30:42.522 INFO  ProgressMeter -  NC_038255.2:5043280              4.3              25782000        5946924.7
06:30:52.527 INFO  ProgressMeter -  NC_038255.2:5230734              4.5              26812000        5955443.0
06:31:02.534 INFO  ProgressMeter -  NC_038255.2:5428240              4.7              27819000        5958384.1
06:31:12.546 INFO  ProgressMeter -  NC_038255.2:5627963              4.8              28826000        5961019.5
06:31:22.551 INFO  ProgressMeter -  NC_038255.2:5816100              5.0              29822000        5961419.3
06:31:32.553 INFO  ProgressMeter -  NC_038255.2:6012495              5.2              30849000        5967848.0
06:31:42.556 INFO  ProgressMeter -  NC_038255.2:6208956              5.3              31883000        5975168.3
06:31:52.559 INFO  ProgressMeter -  NC_038255.2:6394028              5.5              32881000        5975502.6
06:32:02.562 INFO  ProgressMeter -  NC_038255.2:6595440              5.7              33918000        5982696.4
06:32:12.568 INFO  ProgressMeter -  NC_038255.2:6796111              5.8              34962000        5990644.4
06:32:22.567 INFO  ProgressMeter -  NC_038255.2:6988949              6.0              35970000        5992236.9
06:32:32.568 INFO  ProgressMeter -  NC_038255.2:7190730              6.2              36965000        5991620.0
06:32:42.574 INFO  ProgressMeter -  NC_038255.2:7376057              6.3              37962000        5991272.4
06:32:52.575 INFO  ProgressMeter -  NC_038255.2:7595414              6.5              38910000        5983484.3
06:33:02.584 INFO  ProgressMeter -  NC_038255.2:7817963              6.7              39902000        5982563.0
06:33:12.589 INFO  ProgressMeter -  NC_038255.2:8015541              6.8              40894000        5981745.0
06:33:22.598 INFO  ProgressMeter -  NC_038255.2:8192701              7.0              41863000        5977624.8
06:33:32.606 INFO  ProgressMeter -  NC_038255.2:8384530              7.2              42787000        5967434.1
06:33:42.608 INFO  ProgressMeter -  NC_038255.2:8566661              7.3              43751000        5963240.0
06:33:52.609 INFO  ProgressMeter -  NC_038255.2:8758080              7.5              44747000        5963510.2
06:34:02.615 INFO  ProgressMeter -  NC_038255.2:8938187              7.7              45740000        5963312.7
06:34:12.623 INFO  ProgressMeter -  NC_038255.2:9118657              7.8              46677000        5955952.7
06:34:22.659 INFO  ProgressMeter -  NC_038255.2:9305073              8.0              47584000        5944804.7
06:34:32.672 INFO  ProgressMeter -  NC_038255.2:9513984              8.2              48519000        5937818.1
06:34:42.673 INFO  ProgressMeter -  NC_038255.2:9716437              8.3              49465000        5932572.7
06:34:52.681 INFO  ProgressMeter -  NC_038255.2:9907812              8.5              50510000        5939092.3
06:35:02.684 INFO  ProgressMeter - NC_038255.2:10135206              8.7              51469000        5935500.5
06:35:12.698 INFO  ProgressMeter - NC_038255.2:10321448              8.8              52480000        5937804.7
06:35:22.699 INFO  ProgressMeter - NC_038255.2:10524152              9.0              53466000        5937390.1
06:35:32.704 INFO  ProgressMeter - NC_038255.2:10748213              9.2              54326000        5923209.6
06:35:42.710 INFO  ProgressMeter - NC_038255.2:10959773              9.3              55263000        5917770.4
06:35:52.712 INFO  ProgressMeter - NC_038255.2:11267133              9.5              56166000        5908986.5
06:36:02.719 INFO  ProgressMeter - NC_038255.2:11807775              9.7              57036000        5897042.7
06:36:12.721 INFO  ProgressMeter - NC_038255.2:12067257              9.8              57902000        5885147.0
06:36:22.728 INFO  ProgressMeter - NC_038255.2:12257002             10.0              58892000        5885992.1
06:36:32.737 INFO  ProgressMeter - NC_038255.2:12439300             10.2              59901000        5888658.1
06:36:42.737 INFO  ProgressMeter - NC_038255.2:12626553             10.3              60860000        5886487.3
06:36:52.741 INFO  ProgressMeter - NC_038255.2:12862910             10.5              61724000        5875305.4
06:37:02.741 INFO  ProgressMeter - NC_038255.2:13064841             10.7              62743000        5879033.0
06:37:12.741 INFO  ProgressMeter - NC_038255.2:13258624             10.8              63709000        5877756.3
06:37:22.745 INFO  ProgressMeter - NC_038255.2:13460888             11.0              64714000        5880026.2
06:37:32.747 INFO  ProgressMeter - NC_038255.2:13651603             11.2              65727000        5882961.9
06:37:42.756 INFO  ProgressMeter - NC_038255.2:13853539             11.3              66678000        5880291.7
06:37:52.757 INFO  ProgressMeter - NC_038255.2:14060249             11.5              67612000        5876272.5
06:38:02.757 INFO  ProgressMeter - NC_038255.2:14275438             11.7              68527000        5870757.2
06:38:12.760 INFO  ProgressMeter - NC_038255.2:14535303             11.8              69313000        5854476.4
06:38:22.763 INFO  ProgressMeter - NC_038255.2:14749194             12.0              70188000        5846060.7
06:38:32.764 INFO  ProgressMeter - NC_038255.2:14990778             12.2              71108000        5841588.4
06:38:42.767 INFO  ProgressMeter - NC_038255.2:15248939             12.3              72022000        5836734.8
06:38:52.774 INFO  ProgressMeter - NC_038255.2:15449836             12.5              73019000        5838616.3
06:39:02.780 INFO  ProgressMeter - NC_038255.2:15838451             12.7              73526000        5801790.9
06:39:12.790 INFO  ProgressMeter - NC_038255.2:16074652             12.8              74501000        5802341.4
06:39:22.793 INFO  ProgressMeter - NC_038255.2:16263979             13.0              75501000        5804851.9
06:39:32.793 INFO  ProgressMeter - NC_038255.2:16474366             13.2              76461000        5804284.5
06:39:42.801 INFO  ProgressMeter - NC_038255.2:16670739             13.3              77418000        5803455.5
06:39:52.804 INFO  ProgressMeter - NC_038255.2:16866969             13.5              78358000        5801417.1
06:40:02.810 INFO  ProgressMeter - NC_038255.2:17066401             13.7              79349000        5803129.9
06:40:12.817 INFO  ProgressMeter - NC_038255.2:17583653             13.8              80274000        5800039.7
06:40:22.824 INFO  ProgressMeter - NC_038255.2:17910350             14.0              80997000        5782588.1
06:40:32.825 INFO  ProgressMeter - NC_038255.2:18104581             14.2              81980000        5783938.4
06:40:42.839 INFO  ProgressMeter - NC_038255.2:18309499             14.3              82920000        5782171.4
06:40:52.852 INFO  ProgressMeter - NC_038255.2:18541884             14.5              83840000        5779073.1
06:41:02.868 INFO  ProgressMeter - NC_038255.2:18735294             14.7              84783000        5777593.0
06:41:12.876 INFO  ProgressMeter - NC_038255.2:18965118             14.8              85662000        5771885.8
06:41:22.882 INFO  ProgressMeter - NC_038255.2:19198675             15.0              86612000        5771049.0
06:41:32.893 INFO  ProgressMeter - NC_038255.2:19419349             15.2              87575000        5771062.0
06:41:42.903 INFO  ProgressMeter - NC_038255.2:19816995             15.3              88424000        5763637.7
06:41:52.908 INFO  ProgressMeter - NC_038255.2:20087120             15.5              89321000        5759505.3
06:42:02.918 INFO  ProgressMeter - NC_038255.2:20296253             15.7              90301000        5760731.3
06:42:12.918 INFO  ProgressMeter - NC_038255.2:20556367             15.8              91266000        5761033.2
06:42:22.926 INFO  ProgressMeter - NC_038255.2:20752517             16.0              92255000        5762786.0
06:42:32.935 INFO  ProgressMeter - NC_038255.2:20975062             16.2              93246000        5764620.3
06:42:42.944 INFO  ProgressMeter - NC_038255.2:21174153             16.3              94236000        5766356.0
06:42:52.946 INFO  ProgressMeter - NC_038255.2:21366176             16.5              95255000        5769854.0
06:43:02.946 INFO  ProgressMeter - NC_038255.2:21584280             16.7              96239000        5771194.7
06:43:12.955 INFO  ProgressMeter - NC_038255.2:21781969             16.8              97221000        5772344.4
06:43:22.957 INFO  ProgressMeter - NC_038255.2:22095559             17.0              98091000        5766915.3
06:43:32.975 INFO  ProgressMeter - NC_038255.2:22332219             17.2              99025000        5765239.3
06:43:42.980 INFO  ProgressMeter - NC_038255.2:22557607             17.3              99974000        5764521.5
06:43:52.986 INFO  ProgressMeter - NC_038255.2:22755318             17.5             100917000        5763474.6
06:44:02.989 INFO  ProgressMeter - NC_038255.2:22954494             17.7             101858000        5762350.7
06:44:12.994 INFO  ProgressMeter - NC_038255.2:23140102             17.8             102848000        5763983.1
06:44:23.000 INFO  ProgressMeter - NC_038255.2:23347764             18.0             103795000        5763192.5
06:44:33.008 INFO  ProgressMeter - NC_038255.2:23542002             18.2             104781000        5764551.3
06:44:43.014 INFO  ProgressMeter - NC_038255.2:23779687             18.3             105729000        5763824.3
06:44:53.021 INFO  ProgressMeter - NC_038255.2:24019737             18.5             106647000        5761484.6
06:45:03.024 INFO  ProgressMeter - NC_038255.2:24215008             18.7             107669000        5764775.5
06:45:13.030 INFO  ProgressMeter - NC_038255.2:24429778             18.8             108683000        5767568.3
06:45:23.035 INFO  ProgressMeter - NC_038255.2:24634979             19.0             109699000        5770422.4
06:45:33.040 INFO  ProgressMeter - NC_038255.2:24846716             19.2             110695000        5772184.0
06:45:43.042 INFO  ProgressMeter - NC_038255.2:25035123             19.3             111705000        5774653.8
06:45:53.048 INFO  ProgressMeter - NC_038255.2:25226540             19.5             112755000        5779111.9
06:46:03.056 INFO  ProgressMeter - NC_038255.2:25463440             19.7             113682000        5777238.7
06:46:13.068 INFO  ProgressMeter - NC_038255.2:25659673             19.8             114664000        5778139.5
06:46:23.072 INFO  ProgressMeter - NC_038255.2:25849821             20.0             115712000        5782366.7
06:46:33.076 INFO  ProgressMeter - NC_038255.2:26067132             20.2             116682000        5782658.4
06:46:43.076 INFO  ProgressMeter - NC_038255.2:26257373             20.3             117691000        5784881.3
06:46:53.083 INFO  ProgressMeter - NC_038255.2:26457381             20.5             118693000        5786693.9
06:47:03.088 INFO  ProgressMeter - NC_038255.2:26643575             20.7             119720000        5789695.5
06:47:13.106 INFO  ProgressMeter - NC_038255.2:26850339             20.8             120726000        5791581.5
06:47:23.111 INFO  ProgressMeter - NC_038255.2:27050560             21.0             121742000        5793973.2
06:47:33.116 INFO  ProgressMeter - NC_038255.2:27256247             21.2             122736000        5795288.5
06:47:42.432 INFO  CombineGVCFs - Shutting down engine
[March 13, 2024 at 6:47:42 AM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 21.46 minutes.
Runtime.totalMemory()=920649728
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Transport endpoint is not connected
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:48)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.loadNextFeature(FeatureIntervalIterator.java:98)
at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.loadNextNovelFeature(FeatureIntervalIterator.java:74)
at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.next(FeatureIntervalIterator.java:62)
at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.next(FeatureIntervalIterator.java:24)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:408)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:393)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:101)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:165)
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)
Caused by: java.io.IOException: Transport endpoint is not connected
at java.base/java.io.RandomAccessFile.readBytes(Native Method)
at java.base/java.io.RandomAccessFile.read(RandomAccessFile.java:405)
at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:85)
at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:244)
at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:343)
at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:582)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:536)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:479)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:469)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:207)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:215)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:434)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
... 29 more
Using GATK jar /gatk/gatk-package-4.5.0.0-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 /gatk/gatk-package-4.5.0.0-local.jar CombineGVCFs -R ./test/test.fna -V ./gvcf_all.list -L NC_038255.2 -O ./NC_038255.2.merged.g.vcf.gz
total 2.3G
'"-rw-rw-rw- 1 root root  3.6K Dec 13 23:32 GATKConfig.EXAMPLE.properties"
drwxr-xr-x 2 root root  4.0K Mar 13 06:26 GCF_000004515.6_Glycine_max_v4.0
'"-rw-r--r-- 1 root root  1.6G Mar 13 06:47 NC_038255.2.merged.g.vcf.gz"
'"-rw-r--r-- 1 root root   24K Mar 13 06:47 NC_038255.2.merged.g.vcf.gz.tbi"
'"-rw-rw-rw- 1 root root   40K Dec 13 23:32 README.md"
'"-rwxrwxrwx 1 root root   21K Dec 13 23:32 gatk"
'"-rw-rw-rw- 1 root root 1016K Dec 13 23:32 gatk-completion.sh"
'"-rw-rw-rw- 1 root root  422M Dec 13 23:32 gatk-package-4.5.0.0-local.jar"
'"-rw-rw-rw- 1 root root  320M Dec 13 23:32 gatk-package-4.5.0.0-spark.jar"
lrwxrwxrwx 1 root root    36 Dec 13 23:33 gatk-spark.jar -> /gatk/gatk-package-4.5.0.0-spark.jar
lrwxrwxrwx 1 root root    36 Dec 13 23:33 gatk.jar -> /gatk/gatk-package-4.5.0.0-local.jar
'"-rw-rw-rw- 1 root root  117K Dec 13 23:32 gatkPythonPackageArchive.zip"
'"-rw-rw-rw- 1 root root  4.2K Dec 13 23:32 gatkcondaenv.yml"
'"-rw-r--r-- 1 root root    53 Dec 13 23:37 gatkenv.rc"
'"-rw-r--r-- 1 root root  2.3K Mar 13 06:26 gvcf_all.list"
'"-rw-r--r-- 1 root root   866 Dec 13 23:33 run_unit_tests.sh"
drwxrwxrwx 5 root root  4.0K Dec 13 23:32 scripts
'"-rw-r--r-- 1 root root  1.3K Mar 13 06:26 wgs_jcalling_combine_gvcf_job.sh"
Filesystem      Size  Used Avail Use% Mounted on
overlay         100G   13G   88G  13% /
tmpfs            64M     0   64M   0% /dev
tmpfs           7.7G     0  7.7G   0% /sys/fs/cgroup
/dev/nvme0n1p1  100G   13G   88G  13% /etc/hosts
shm              64M     0   64M   0% /dev/shm
wgs-pipeline    1.0P     0  1.0P   0% /mnt

Thank you very much