I get the following error with GATK 4.1.8.1 when running SplitNCigarReads after MarkDuplicates on RNA-seq data:

java.lang.IllegalArgumentException: contig must be non-null and not equal to *, and start must be >= 1

The command I used was the following (I did not include the full path to the files):

gatk SplitNCigarReads -R /home/data/hg38_GRCh38.97_nobackup/hg38_primary_refseq.fa -I /home/results/SOD1/results/5_GATK_dedupSplit/SOD1P_A272C_rep2/SOD1P_A272C_rep2.Dedup.bam -O /home/results/SOD1/results/5_GATK_dedupSplit/SOD1P_A272C_rep2/SOD1P_A272C_rep2.Split.bam

Here the log:

11:08:24.240 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/results/SOD1/.snakemake/conda/93139e1d/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 19, 2020 11:08:25 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:08:25.663 INFO SplitNCigarReads - ------------------------------------------------------------
11:08:25.663 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.1.8.1
11:08:25.663 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
11:08:25.664 INFO SplitNCigarReads - Executing as giulia@### on Linux v2.6.32-754.31.1.el6.x86_64 amd64
11:08:25.664 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
11:08:25.664 INFO SplitNCigarReads - Start Date/Time: August 19, 2020 11:08:24 AM CEST
11:08:25.664 INFO SplitNCigarReads - ------------------------------------------------------------
11:08:25.664 INFO SplitNCigarReads - ------------------------------------------------------------
11:08:25.668 INFO SplitNCigarReads - HTSJDK Version: 2.23.0
11:08:25.668 INFO SplitNCigarReads - Picard Version: 2.22.8
11:08:25.668 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:08:25.668 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:08:25.668 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:08:25.668 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:08:25.668 INFO SplitNCigarReads - Deflater: IntelDeflater
11:08:25.669 INFO SplitNCigarReads - Inflater: IntelInflater
11:08:25.669 INFO SplitNCigarReads - GCS max retries/reopens: 20
11:08:25.669 INFO SplitNCigarReads - Requester pays: disabled
11:08:25.669 INFO SplitNCigarReads - Initializing engine
11:08:27.485 INFO SplitNCigarReads - Done initializing engine
11:08:27.777 INFO ProgressMeter - Starting traversal
11:08:27.777 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
11:08:37.798 INFO ProgressMeter - chr10:46550267 0.2 214000 1283614.9
11:08:47.783 INFO ProgressMeter - chr10:78009888 0.3 437000 1310606.8
11:08:57.791 INFO ProgressMeter - chr10:100523922 0.5 666000 1331378.7
11:09:07.810 INFO ProgressMeter - chr10:124988912 0.7 894000 1339894.6
11:09:17.907 INFO ProgressMeter - unmapped 0.8 1123000 1344105.3
11:09:27.935 INFO ProgressMeter - chr11:46381732 1.0 1335000 1331493.7
11:09:37.983 INFO ProgressMeter - chr11:62571018 1.2 1563000 1335783.3
11:09:47.999 INFO ProgressMeter - chr11:65855361 1.3 1775000 1327566.0
11:09:58.036 INFO ProgressMeter - chr11:75404041 1.5 1979000 1315547.5
11:10:08.060 INFO ProgressMeter - chr11:113405221 1.7 2200000 1316288.1
11:10:18.066 INFO ProgressMeter - chr11:130915630 1.8 2412000 1312188.9
11:10:28.109 INFO ProgressMeter - chr12:8334698 2.0 2634000 1313366.4
11:10:38.135 INFO ProgressMeter - chr12:49002681 2.2 2852000 1312702.8
11:10:48.161 INFO ProgressMeter - chr12:49185513 2.3 2990000 1277923.4
11:10:58.278 INFO ProgressMeter - chr12:49186371 2.5 3073000 1225108.1
11:11:08.319 INFO ProgressMeter - chr12:51994412 2.7 3188000 1191463.9
11:11:18.370 INFO ProgressMeter - chr12:56174759 2.8 3405000 1197587.2
11:11:28.409 INFO ProgressMeter - chr12:76053272 3.0 3612000 1199787.4
11:11:38.445 INFO ProgressMeter - chr12:111709551 3.2 3827000 1204292.3
11:11:48.485 INFO ProgressMeter - chr12:123737064 3.3 4046000 1209518.3
11:11:58.523 INFO ProgressMeter - chr13:37001074 3.5 4292000 1221944.9
11:12:08.538 INFO ProgressMeter - chr13:110462171 3.7 4490000 1220329.8
11:12:18.546 INFO ProgressMeter - chr14:39148146 3.8 4729000 1229546.6
11:12:28.576 INFO ProgressMeter - chr14:70642455 4.0 4947000 1232651.4
11:12:38.753 INFO ProgressMeter - chr14:100293540 4.2 5168000 1235496.6
11:12:48.762 INFO ProgressMeter - chr15:26547806 4.3 5409000 1243519.7
11:12:58.792 INFO ProgressMeter - chr15:48159630 4.5 5618000 1243768.8
11:13:08.805 INFO ProgressMeter - chr15:66503406 4.7 5836000 1245996.8
11:13:18.815 INFO ProgressMeter - chr15:78111219 4.9 6076000 1252619.9
11:13:28.829 INFO ProgressMeter - chr15:88464852 5.0 6293000 1254201.9
11:13:38.842 INFO ProgressMeter - chr16:1962894 5.2 6537000 1260898.1
11:13:48.864 INFO ProgressMeter - chr16:14676258 5.4 6752000 1261714.1
11:13:58.905 INFO ProgressMeter - chr16:28366124 5.5 6967000 1262412.1
11:14:08.947 INFO ProgressMeter - chr16:49526522 5.7 7180000 1262713.6
11:14:18.962 INFO ProgressMeter - chr16:70299327 5.9 7394000 1263269.4
11:14:28.995 INFO ProgressMeter - chr16:89668693 6.0 7626000 1266717.8
11:14:39.025 INFO ProgressMeter - chr17:4973677 6.2 7891000 1275320.0
11:14:49.045 INFO ProgressMeter - chr17:16381983 6.4 8109000 1276110.2
11:14:59.054 INFO ProgressMeter - chr17:30477440 6.5 8330000 1277355.9
11:15:09.060 INFO ProgressMeter - chr17:41757691 6.7 8558000 1279595.7
11:15:19.061 INFO ProgressMeter - chr17:47676439 6.9 8771000 1279553.8
11:15:29.136 INFO ProgressMeter - chr17:61034712 7.0 8999000 1281425.1
11:15:39.180 INFO ProgressMeter - chr17:75851570 7.2 9210000 1280936.9
11:15:49.216 INFO ProgressMeter - chr17:81512052 7.4 9440000 1283076.5
11:16:00.645 INFO ProgressMeter - chr18:31837983 7.5 9667000 1284773.5
11:16:09.289 INFO ProgressMeter - chr18:57476495 7.7 9857000 1281483.5
11:16:19.312 INFO ProgressMeter - chr19:1272728 7.9 10080000 1282622.2
11:16:29.351 INFO ProgressMeter - chr19:3977584 8.0 10290000 1282046.0
11:16:39.352 INFO ProgressMeter - chr19:7542597 8.2 10474000 1278424.0
11:16:49.359 INFO ProgressMeter - chr19:12715306 8.4 10686000 1278275.5
11:16:59.379 INFO ProgressMeter - chr19:18576397 8.5 10899000 1278222.7
11:17:09.380 INFO ProgressMeter - chr19:36236363 8.7 11118000 1278903.7
11:17:19.387 INFO ProgressMeter - chr19:42301982 8.9 11334000 1279208.4
11:17:29.421 INFO ProgressMeter - chr19:48966389 9.0 11558000 1280324.3
11:17:39.451 INFO ProgressMeter - chr19:54179790 9.2 11761000 1279127.3
11:17:49.455 INFO ProgressMeter - chr1:1218873 9.4 12017000 1283691.5
11:17:59.479 INFO ProgressMeter - chr1:10296609 9.5 12222000 1282696.2
11:18:09.514 INFO ProgressMeter - chr1:23692625 9.7 12447000 1283776.0
11:18:19.525 INFO ProgressMeter - chr1:32680380 9.9 12681000 1285783.8
11:18:29.579 INFO ProgressMeter - chr1:43440032 10.0 12908000 1286934.9
11:18:39.604 INFO ProgressMeter - chr1:70246892 10.2 13127000 1287326.8
11:18:49.666 INFO ProgressMeter - chr1:111756675 10.4 13343000 1287414.5
11:18:59.652 INFO ProgressMeter - chr1:150629436 10.5 13548000 1286457.0
11:19:09.660 INFO ProgressMeter - chr1:156082208 10.7 13767000 1286870.0
11:19:19.661 INFO ProgressMeter - chr1:176027680 10.9 14001000 1288664.9
11:19:29.687 INFO ProgressMeter - chr1:204979021 11.0 14213000 1288362.5
11:19:39.687 INFO ProgressMeter - chr1:228647139 11.2 14442000 1289637.0
11:19:49.728 INFO ProgressMeter - chr20:19956671 11.4 14692000 1292646.1
11:19:59.760 INFO ProgressMeter - chr20:38570827 11.5 14923000 1293933.5
11:20:09.777 INFO ProgressMeter - chr20:58910900 11.7 15138000 1293848.0
11:20:19.803 INFO ProgressMeter - chr21:33355512 11.9 15407000 1298295.3
11:20:29.811 INFO ProgressMeter - chr22:20142910 12.0 15651000 1300575.9
11:20:39.876 INFO ProgressMeter - chr22:31716754 12.2 15886000 1301955.1
11:20:49.901 INFO ProgressMeter - chr22:41168540 12.4 16121000 1303368.8
11:20:59.919 INFO ProgressMeter - chr2:264379 12.5 16341000 1303557.0
11:21:09.925 INFO ProgressMeter - chr2:27441904 12.7 16627000 1308958.4
11:21:19.960 INFO ProgressMeter - chr2:61204558 12.9 16842000 1308653.5
11:21:30.010 INFO ProgressMeter - chr2:84906053 13.0 17049000 1307717.8
11:21:40.036 INFO ProgressMeter - chr2:107997940 13.2 17266000 1307602.7
11:21:50.068 INFO ProgressMeter - chr2:148949859 13.4 17461000 1305835.4
11:22:00.092 INFO ProgressMeter - chr2:181929795 13.5 17669000 1305084.9
11:22:10.129 INFO ProgressMeter - chr2:215404395 13.7 17877000 1304333.6
11:22:20.144 INFO ProgressMeter - chr2:233476964 13.9 18086000 1303703.8
11:22:30.161 INFO ProgressMeter - chr3:18378283 14.0 18328000 1305437.9
11:22:40.198 INFO ProgressMeter - chr3:47577563 14.2 18546000 1305411.3
11:22:50.212 INFO ProgressMeter - chr3:52290060 14.4 18765000 1305489.7
11:23:00.245 INFO ProgressMeter - chr3:105732819 14.5 18969000 1304506.3
11:23:10.272 INFO ProgressMeter - chr3:135134568 14.7 19196000 1305119.4
11:23:20.300 INFO ProgressMeter - chr3:184180967 14.9 19416000 1305243.7
11:23:30.329 INFO ProgressMeter - chr4:3023521 15.0 19667000 1307426.1
11:23:40.369 INFO ProgressMeter - chr4:39082019 15.2 19904000 1308624.2
11:23:50.384 INFO ProgressMeter - chr4:80199167 15.4 20125000 1308791.3
11:24:00.414 INFO ProgressMeter - chr4:143214407 15.5 20333000 1308097.4
11:24:10.437 INFO ProgressMeter - chr5:11159670 15.7 20570000 1309273.8
11:24:20.453 INFO ProgressMeter - chr5:62512314 15.9 20797000 1309805.2
11:24:30.457 INFO ProgressMeter - chr5:81233779 16.0 21043000 1311527.5
11:24:40.580 INFO ProgressMeter - chr5:132879197 16.2 21260000 1311262.4
11:24:50.607 INFO ProgressMeter - chr5:147393146 16.4 21492000 1312049.2
11:25:00.629 INFO ProgressMeter - chr5:175881189 16.5 21720000 1312582.3
11:25:10.725 INFO ProgressMeter - chr6:3154899 16.7 21966000 1314086.1
11:25:20.752 INFO ProgressMeter - chr6:21594830 16.9 22176000 1313517.1
11:25:30.759 INFO ProgressMeter - chr6:30724438 17.0 22372000 1312163.9
11:25:40.782 INFO ProgressMeter - chr6:34245857 17.2 22562000 1310469.3
11:25:50.793 INFO ProgressMeter - chr6:44302847 17.4 22748000 1308589.7
11:26:00.812 INFO ProgressMeter - chr6:73519370 17.6 22975000 1309073.3
11:26:10.812 INFO ProgressMeter - chr6:106971626 17.7 23160000 1307200.6
11:26:20.860 INFO ProgressMeter - chr6:132816490 17.9 23332000 1304577.6
11:26:30.883 INFO ProgressMeter - chr7:4835033 18.1 23568000 1305578.6
11:26:40.920 INFO ProgressMeter - chr7:19722039 18.2 23766000 1304460.0
11:26:50.934 INFO ProgressMeter - chr7:43444529 18.4 23946000 1302407.5
11:27:00.980 INFO ProgressMeter - chr7:73266688 18.6 24120000 1300032.4
11:27:11.000 INFO ProgressMeter - chr7:80919065 18.7 24315000 1298851.6
11:27:21.228 INFO ProgressMeter - chr7:100376126 18.9 24485000 1296130.1
11:27:31.230 INFO ProgressMeter - chr7:128463115 19.1 24646000 1293241.9
11:27:41.260 INFO ProgressMeter - chr7:148760447 19.2 24829000 1291514.5
11:27:51.305 INFO ProgressMeter - chr8:15650779 19.4 25035000 1290987.4
11:28:01.341 INFO ProgressMeter - chr8:24917812 19.6 25210000 1288894.3
11:28:11.358 INFO ProgressMeter - chr8:30066841 19.7 25442000 1289747.0
11:28:21.381 INFO ProgressMeter - chr8:73292699 19.9 25663000 1290026.9
11:28:31.396 INFO ProgressMeter - chr8:103324502 20.1 25883000 1290258.8
11:28:41.445 INFO ProgressMeter - chr8:144527762 20.2 26044000 1287536.0
11:28:51.473 INFO ProgressMeter - chr9:35381559 20.4 26255000 1287329.5
11:29:01.508 INFO ProgressMeter - chr9:87681729 20.6 26442000 1285952.9
11:29:11.564 INFO ProgressMeter - chr9:113180755 20.7 26623000 1284287.4
11:29:21.611 INFO ProgressMeter - chr9:128504872 20.9 26795000 1282227.2
11:29:31.697 INFO ProgressMeter - chr9:133350644 21.1 27009000 1282193.5
11:29:41.709 INFO ProgressMeter - chrM:5205 21.2 27203000 1281214.4
11:29:52.519 INFO ProgressMeter - chrM:6157 21.4 27334000 1276553.0
11:30:02.535 INFO ProgressMeter - chrM:6628 21.6 27420000 1270662.2
11:30:12.655 INFO ProgressMeter - chrM:7002 21.7 27488000 1263934.3
11:30:22.794 INFO ProgressMeter - chrM:7613 21.9 27546000 1256835.5
11:30:32.876 INFO ProgressMeter - chrM:8148 22.1 27598000 1249628.3
11:30:43.034 INFO ProgressMeter - chrM:8685 22.3 27653000 1242593.2
11:30:53.231 INFO ProgressMeter - chrM:9153 22.4 27699000 1235226.2
11:31:03.273 INFO ProgressMeter - chrM:9585 22.6 27746000 1228155.6
11:31:13.586 INFO ProgressMeter - chrM:10556 22.8 27799000 1221210.3
11:31:23.642 INFO ProgressMeter - chrX:3604631 22.9 27890000 1216253.9
11:31:33.681 INFO ProgressMeter - chrX:41167498 23.1 28067000 1215105.8
11:31:43.739 INFO ProgressMeter - chrX:49122395 23.3 28226000 1213185.8
11:31:53.742 INFO ProgressMeter - chrX:74591500 23.4 28429000 1213217.4
11:32:03.755 INFO ProgressMeter - chrX:111297421 23.6 28679000 1215230.7
11:32:13.759 INFO ProgressMeter - chrX:136873741 23.8 28896000 1215836.7
11:32:23.774 INFO ProgressMeter - chrX:154468181 23.9 29072000 1214710.1
11:32:33.774 INFO ProgressMeter - unmapped 24.1 29988000 1244317.9
11:32:43.779 INFO ProgressMeter - unmapped 24.3 31063000 1280066.9
11:32:53.799 INFO ProgressMeter - unmapped 24.4 32134000 1315151.7
11:33:03.809 INFO ProgressMeter - unmapped 24.6 33217000 1350255.3
11:33:13.935 INFO ProgressMeter - unmapped 24.8 34309000 1385142.1
11:33:20.962 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter

11:33:21.292 INFO OverhangFixingManager - Overhang Fixing Manager saved 112537 reads in the first pass
11:33:21.294 INFO SplitNCigarReads - Starting traversal pass 2
11:33:23.982 INFO ProgressMeter - chr10:12196227 24.9 35147000 1409445.9
11:33:34.237 INFO ProgressMeter - chr10:48420422 25.1 35314000 1406503.6
11:33:44.278 INFO ProgressMeter - chr10:73765059 25.3 35485000 1403955.6
11:33:54.338 INFO ProgressMeter - chr10:86960896 25.4 35597000 1399105.6
11:34:04.366 INFO ProgressMeter - chr10:100983991 25.6 35764000 1396495.7
11:34:16.954 INFO ProgressMeter - chr10:119136470 25.8 35937000 1391848.7
11:34:26.969 INFO ProgressMeter - chr11:1275835 26.0 36103000 1389296.5
11:34:39.760 INFO ProgressMeter - chr11:10807277 26.2 36260000 1383984.4
11:34:49.774 INFO ProgressMeter - chr11:47164399 26.4 36445000 1382240.3
11:34:59.804 INFO ProgressMeter - chr11:62392956 26.5 36628000 1380429.7
11:35:10.457 INFO ProgressMeter - chr11:63988685 26.7 36741000 1375483.6
11:35:20.564 INFO ProgressMeter - chr11:66272230 26.9 36900000 1372778.9
11:35:33.097 INFO ProgressMeter - chr11:72007535 27.1 37005000 1366069.5
11:35:43.119 INFO ProgressMeter - chr11:95172986 27.3 37179000 1364081.6
11:35:53.151 INFO ProgressMeter - chr11:117223907 27.4 37338000 1361562.8
11:36:03.190 INFO ProgressMeter - chr11:123606973 27.6 37452000 1357437.7
11:36:13.237 INFO ProgressMeter - chr12:6603567 27.8 37633000 1355770.4
11:36:23.243 INFO ProgressMeter - chr12:11047139 27.9 37742000 1351576.2
11:36:33.703 INFO ProgressMeter - chr12:46363050 28.1 37900000 1348813.6
11:36:43.972 INFO ProgressMeter - chr12:49184970 28.3 38019000 1344857.2
11:36:54.038 INFO ProgressMeter - chr12:49185749 28.4 38107000 1340017.7
11:37:05.558 INFO ProgressMeter - chr12:49186322 28.6 38150000 1332533.9
11:37:15.589 INFO ProgressMeter - chr12:49186786 28.8 38203000 1326637.4
11:37:25.607 INFO ProgressMeter - chr12:54132075 29.0 38354000 1324203.2
11:37:35.669 INFO ProgressMeter - chr12:56117647 29.1 38469000 1320527.8
11:37:45.685 INFO ProgressMeter - chr12:58587859 29.3 38627000 1318396.6
11:37:55.686 INFO ProgressMeter - chr12:98734352 29.5 38801000 1316843.8
11:38:05.707 INFO ProgressMeter - chr12:112172781 29.6 38930000 1313775.0
11:38:16.059 INFO ProgressMeter - chr12:122060222 29.8 39095000 1311705.9
11:38:26.069 INFO ProgressMeter - chr12:130793251 30.0 39223000 1308675.8
11:38:36.128 INFO ProgressMeter - chr13:41358927 30.1 39395000 1307102.4
11:38:46.139 INFO ProgressMeter - chr13:100625609 30.3 39545000 1304856.4
11:38:56.154 INFO ProgressMeter - chr14:21085819 30.5 39649000 1301121.2
11:39:06.172 INFO ProgressMeter - chr14:45175522 30.6 39833000 1300036.2
11:39:16.179 INFO ProgressMeter - chr14:64209482 30.8 39983000 1297867.0
11:39:26.185 INFO ProgressMeter - chr14:90406787 31.0 40162000 1296658.2
11:39:37.084 INFO ProgressMeter - chr14:102049458 31.2 40306000 1293720.1
11:39:47.128 INFO ProgressMeter - chr15:24975501 31.3 40472000 1292105.6
11:39:57.129 INFO ProgressMeter - chr15:43523841 31.5 40648000 1290856.0
11:40:07.133 INFO ProgressMeter - chr15:52752308 31.7 40771000 1287941.8
11:40:17.174 INFO ProgressMeter - chr15:67542771 31.8 40930000 1286165.2
11:40:29.159 INFO ProgressMeter - chr15:74135970 32.0 41061000 1282234.0
11:40:39.187 INFO ProgressMeter - chr15:78774665 32.2 41228000 1280764.5
11:40:49.262 INFO ProgressMeter - chr15:88899212 32.4 41386000 1279000.4
11:40:59.285 INFO ProgressMeter - chr16:138189 32.5 41526000 1276735.7
11:41:09.291 INFO ProgressMeter - chr16:2770628 32.7 41712000 1275912.4
11:41:19.294 INFO ProgressMeter - chr16:14884438 32.9 41847000 1273547.2
11:41:29.560 INFO ProgressMeter - chr16:27528716 33.0 42034000 1272611.6
11:41:41.018 INFO ProgressMeter - chr16:30784045 33.2 42206000 1270473.6
11:41:51.255 INFO ProgressMeter - chr16:58512654 33.4 42371000 1268923.3
11:42:01.283 INFO ProgressMeter - chr16:72282546 33.6 42516000 1266924.5
11:42:11.339 INFO ProgressMeter - chr16:85661748 33.7 42635000 1264157.0
11:42:21.348 INFO ProgressMeter - chr16:89935324 33.9 42791000 1262537.7
11:42:32.205 INFO ProgressMeter - chr17:4307056 34.1 42952000 1260558.0
11:42:42.745 INFO ProgressMeter - chr17:7903977 34.2 43107000 1258618.1
11:42:52.775 INFO ProgressMeter - chr17:19677273 34.4 43279000 1257502.4
11:43:02.815 INFO ProgressMeter - chr17:29121170 34.6 43396000 1254801.1
11:43:12.979 INFO ProgressMeter - chr17:38742069 34.8 43558000 1253346.2
11:43:22.998 INFO ProgressMeter - chr17:41972016 34.9 43676000 1250732.0
11:43:33.012 INFO ProgressMeter - chr17:46026157 35.1 43825000 1249029.2
11:43:43.217 INFO ProgressMeter - chr17:50978705 35.3 43993000 1247768.8
11:43:53.252 INFO ProgressMeter - chr17:63820852 35.4 44126000 1245632.2
11:44:03.290 INFO ProgressMeter - chr17:75849619 35.6 44299000 1244637.7
11:44:15.653 INFO ProgressMeter - chr17:81510030 35.8 44439000 1241384.5
11:44:26.207 INFO ProgressMeter - chr17:82084551 36.0 44599000 1239762.2
11:44:38.378 INFO ProgressMeter - chr18:34806219 36.2 44765000 1237399.2
11:44:48.841 INFO ProgressMeter - chr18:57029481 36.4 44936000 1236167.3
11:44:58.842 INFO ProgressMeter - chr19:919526 36.5 45115000 1235426.6
11:45:08.844 INFO ProgressMeter - chr19:1778170 36.7 45247000 1233410.9
11:45:18.878 INFO ProgressMeter - chr19:3979399 36.9 45395000 1231829.8
11:45:32.031 INFO ProgressMeter - chr19:6213788 37.1 45523000 1227998.2
11:45:42.075 INFO ProgressMeter - chr19:10718184 37.2 45682000 1226747.7
11:45:52.107 INFO ProgressMeter - chr19:14413080 37.4 45837000 1225408.6
11:46:02.153 INFO ProgressMeter - chr19:18230947 37.6 45955000 1223088.4
11:46:12.898 INFO ProgressMeter - chr19:32615767 37.8 46106000 1221285.8
11:46:22.928 INFO ProgressMeter - chr19:37699195 37.9 46231000 1219198.7
11:46:32.955 INFO ProgressMeter - chr19:41956825 38.1 46376000 1217655.7
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11:47:23.674 INFO ProgressMeter - chr1:1049287 38.9 47096000 1209711.4
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11:49:44.229 INFO ProgressMeter - chr1:180884053 41.3 49124000 1190186.6
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11:50:34.364 INFO ProgressMeter - chr20:21755247 42.1 49791000 1182409.3
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11:52:06.801 INFO ProgressMeter - chr22:36506016 43.7 51037000 1169222.3
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11:52:26.876 INFO ProgressMeter - chr22:45197841 44.0 51332000 1167034.7
11:52:36.972 INFO ProgressMeter - chr2:2821262 44.2 51447000 1165191.7
11:52:46.983 INFO ProgressMeter - chr2:25247121 44.3 51636000 1165069.6
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11:53:07.023 INFO ProgressMeter - chr2:55050009 44.7 51895000 1162155.3
11:53:17.140 INFO ProgressMeter - chr2:70979679 44.8 52040000 1161018.4
11:53:27.698 INFO ProgressMeter - chr2:84906488 45.0 52151000 1158945.0
11:53:37.751 INFO ProgressMeter - chr2:101004257 45.2 52312000 1158210.4
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11:55:00.579 INFO ProgressMeter - chr3:18416038 46.5 53418000 1147621.6
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11:56:32.887 INFO ProgressMeter - chr3:196828468 48.1 54639000 1136296.4
11:56:42.895 INFO ProgressMeter - chr4:4409601 48.3 54777000 1135228.3
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11:58:55.195 INFO ProgressMeter - chr5:149259532 50.5 56610000 1121946.2
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11:59:15.244 INFO ProgressMeter - chr5:178210876 50.8 56895000 1120176.2
11:59:25.257 INFO ProgressMeter - chr6:3154192 51.0 57012000 1118803.7
11:59:35.293 INFO ProgressMeter - chr6:3226636 51.1 57186000 1118546.7
11:59:45.310 INFO ProgressMeter - chr6:30284655 51.3 57345000 1118005.9
11:59:55.314 INFO ProgressMeter - chr6:30899952 51.5 57483000 1117065.2
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12:02:59.520 INFO ProgressMeter - chr8:70396 54.5 60027000 1100826.1
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12:04:31.512 INFO ProgressMeter - chr9:35398228 56.1 61346000 1094247.9
12:04:41.520 INFO ProgressMeter - chr9:83309264 56.2 61484000 1093456.1
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12:05:03.494 INFO ProgressMeter - chr9:124353531 56.6 61780000 1091610.7
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12:05:43.640 INFO ProgressMeter - chrM:5766 57.3 62312000 1088145.8
12:05:53.748 INFO ProgressMeter - chrM:6064 57.4 62385000 1086225.0
12:06:03.811 INFO ProgressMeter - chrM:6456 57.6 62473000 1084590.0
12:06:14.164 INFO ProgressMeter - chrM:6782 57.8 62539000 1082493.1
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12:06:34.386 INFO ProgressMeter - chrM:7892 58.1 62661000 1078314.2
12:06:44.407 INFO ProgressMeter - chrM:8526 58.3 62714000 1076133.3
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12:07:04.855 INFO ProgressMeter - chrM:9385 58.6 62814000 1071582.7
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12:07:24.914 INFO ProgressMeter - chrM:10943 59.0 62904000 1067032.5
12:07:34.942 INFO ProgressMeter - chrX:12975129 59.1 63028000 1066113.4
12:07:44.971 INFO ProgressMeter - chrX:41349821 59.3 63179000 1065654.6
12:07:54.982 INFO ProgressMeter - chrX:48923158 59.5 63296000 1064631.8
12:08:05.013 INFO ProgressMeter - chrX:68535195 59.6 63444000 1064128.8
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12:08:25.159 INFO ProgressMeter - chrX:111294586 60.0 63723000 1062822.9
12:08:35.207 INFO ProgressMeter - chrX:129516349 60.1 63932000 1063338.7
12:08:45.361 INFO ProgressMeter - chrX:153743608 60.3 64037000 1062095.6
12:08:56.075 INFO ProgressMeter - chrY:302910 60.5 64182000 1061357.1
12:13:04.075 INFO SplitNCigarReads - Shutting down engine
[August 19, 2020 12:13:04 PM CEST] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 64.67 minutes.
Runtime.totalMemory()=11648630784
java.lang.IllegalArgumentException: contig must be non-null and not equal to *, and start must be >= 1
at org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter.setMatePosition(SAMRecordToGATKReadAdapter.java:197)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.setPredictedMateInformation(OverhangFixingManager.java:445)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.splitNCigarRead(SplitNCigarReads.java:212)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.lambda$traverseReads$1(SplitNCigarReads.java:181)
at org.broadinstitute.hellbender.engine.MultiplePassReadWalker.lambda$forEachRead$0(MultiplePassReadWalker.java:60)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.MultiplePassReadWalker.forEachRead(MultiplePassReadWalker.java:58)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.traverseReads(SplitNCigarReads.java:180)
at org.broadinstitute.hellbender.engine.MultiplePassReadWalker.traverse(MultiplePassReadWalker.java:74)
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/results/SOD1/.snakemake/conda/93139e1d/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/results/SOD1/.snakemake/conda/93139e1d/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar SplitNCigarReads -R /home/data/hg38_GRCh38.97_nobackup/hg38_primary_refseq.fa -I /home/results/SOD1/results/5_GATK_dedupSplit/SOD1P_A272C_rep2/SOD1P_A272C_rep2.Dedup.bam -O /home/results/SOD1/results/5_GATK_dedupSplit/SOD1P_A272C_rep2/SOD1P_A272C_rep2.Split.bam

Do you have any suggestion about how to solve this?

Thank you very much,

Giulia