Class picard.sam.ValidateSamFileTest

all > picard.sam > ValidateSamFileTest

tests

failures

ignored

0.065s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testIndex[0](index_test_b.bam, 0)	0.008s	passed
testIndex[1](index_test_c.bam, 0)	0.015s	passed
test[0](nofile, -1)	0.006s	passed
test[1](good/sorted-pair.sam, 0)	0.005s	passed
test[2](good/sorted-pair-v1.6.sam, 0)	0.006s	passed
test[3](bad/unpaired-mate.sam, 3)	0.005s	passed
test[4](bad/missing-rg-info.sam, 2)	0.007s	passed
test[5](bad/missing-rg-info-v1.6.sam, 2)	0.007s	passed
test[6](bad/sorted-pair-missing-rg.sam, 1)	0.006s	passed

Standard output

No errors found
No errors found
ERROR::MATE_NOT_FOUND:Read name bar:record:6, Mate not found for paired read
ERROR::MISSING_READ_GROUP:Read groups is empty
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group
Maximum output of [100] errors reached.
ERROR::MISSING_READ_GROUP:Read groups is empty
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group
WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group
Maximum output of [100] errors reached.
WARNING::RECORD_MISSING_READ_GROUP:Read name bar:record:1, A record is missing a read group
No errors found
No errors found

Standard error

[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/nofile --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
ERROR	2025-04-24 13:04:15	ValidateSamFile	Cannot read non-existent file: file:///mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/nofile
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/good/sorted-pair.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/good/sorted-pair-v1.6.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/bad/unpaired-mate.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info-v1.6.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/ValidateSamFile/bad/sorted-pair-missing-rg.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SortSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_b.bam --SORT_ORDER coordinate --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:15	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_b.bam --IGNORE MISSING_PLATFORM_VALUE --IGNORE MISMATCH_MATE_ALIGNMENT_START --IGNORE MISSING_TAG_NM --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
WARNING: BAM index file /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_b.bam.bai is older than BAM /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_b.bam
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SortSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_c.bam --SORT_ORDER coordinate --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:15	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_c.bam --IGNORE MISSING_PLATFORM_VALUE --IGNORE MISMATCH_MATE_ALIGNMENT_START --IGNORE MISSING_TAG_NM --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:04:15	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
WARNING: BAM index file /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_c.bam.csi is older than BAM /mounts/lovelace/software/picard/picard/testdata/picard/indices/index_test_c.bam
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824