Pilon terminated with "Exception in thread "main" java.lang.reflect.InvocationTargetException" error

[jnarayan81]

MyPassport: java -Xmx32G -jar /home/urbe/anaconda3/share/pilon-1.22-0/pilon-1.22.jar --genome MatDATA/final_edited.fa --unpaired ngmlrMAP_ONT.sorted.bam  --changes --variant --tracks --outdir seeTEST
Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400
Genome: MatDATA/final_edited.fa
Fixing breaks, indels, gaps, local, snps
Input genome size: 185688181
Scanning BAMs
ngmlrMAP_ONT.sorted.bam: 2280512 reads, 0 filtered, 1693834 mapped, 0 proper, 0 stray, Unpaired 100% 12353+/-8282, max 37198
Processing i33C-assembly_contig_1030:1-1103
unpaired ngmlrMAP_ONT.sorted.bam: coverage 108
Total Reads: 119, Coverage: 108, minDepth: 11
Confirmed 1024 of 1103 bases (92.84%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_1030:1-1103 log:
Finished processing i33C-assembly_contig_1030:1-1103
Processing i33C-assembly_contig_118:1-596
unpaired ngmlrMAP_ONT.sorted.bam: coverage 9
Total Reads: 10, Coverage: 9, minDepth: 5
Confirmed 503 of 596 bases (84.40%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_118:1-596 log:
Finished processing i33C-assembly_contig_118:1-596
Processing i33C-assembly_contig_1109:1-17939
unpaired ngmlrMAP_ONT.sorted.bam: coverage 48
Total Reads: 220, Coverage: 48, minDepth: 5
Confirmed 16127 of 17939 bases (89.90%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 26 small deletions totaling 30 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_1109:472-488 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:8173 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:9619 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:9929 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:10933-12321 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:14874-14875 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1109:15937 0 -0 +0 NoSolution
i33C-assembly_contig_1109:1-17939 log:
Finished processing i33C-assembly_contig_1109:1-17939
Processing i33C-assembly_contig_1108:1-2195
unpaired ngmlrMAP_ONT.sorted.bam: coverage 66
Total Reads: 148, Coverage: 66, minDepth: 7
Confirmed 1860 of 2195 bases (84.74%)
Corrected 2 snps; 0 ambiguous bases; corrected 2 small insertions totaling 2 bases, 7 small deletions totaling 9 bases
i33C-assembly_contig_1108:1-2195 log:
Finished processing i33C-assembly_contig_1108:1-2195
Processing i33C-assembly_contig_1088:1-1151
unpaired ngmlrMAP_ONT.sorted.bam: coverage 124
Total Reads: 222, Coverage: 124, minDepth: 12
Confirmed 1058 of 1151 bases (91.92%)
Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 2 bases
i33C-assembly_contig_1088:1-1151 log:
Finished processing i33C-assembly_contig_1088:1-1151
Processing i33C-assembly_contig_584:1-214
unpaired ngmlrMAP_ONT.sorted.bam: coverage 8
Total Reads: 8, Coverage: 8, minDepth: 5
Confirmed 158 of 214 bases (73.83%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_584:1-214 log:
Finished processing i33C-assembly_contig_584:1-214
Processing i33C-assembly_contig_589:1-6076
unpaired ngmlrMAP_ONT.sorted.bam: coverage 34
Total Reads: 64, Coverage: 34, minDepth: 5
Confirmed 5750 of 6076 bases (94.63%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 2 bases
i33C-assembly_contig_589:1-6076 log:
Finished processing i33C-assembly_contig_589:1-6076
Processing i33C-assembly_contig_999:1-2638
unpaired ngmlrMAP_ONT.sorted.bam: coverage 15
Total Reads: 17, Coverage: 15, minDepth: 5
Confirmed 2327 of 2638 bases (88.21%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 9 small deletions totaling 10 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_999:169-170 0 -0 +0 NoSolution
i33C-assembly_contig_999:1-2638 log:
Finished processing i33C-assembly_contig_999:1-2638
Processing i33C-assembly_contig_119:1-3737
unpaired ngmlrMAP_ONT.sorted.bam: coverage 46
Total Reads: 117, Coverage: 46, minDepth: 5
Confirmed 3188 of 3737 bases (85.31%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 6 bases
i33C-assembly_contig_119:1-3737 log:
Finished processing i33C-assembly_contig_119:1-3737
Processing i33C-assembly_contig_628:1-1946
unpaired ngmlrMAP_ONT.sorted.bam: coverage 22
Total Reads: 33, Coverage: 22, minDepth: 5
Confirmed 1593 of 1946 bases (81.86%)
Corrected 3 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 4 small deletions totaling 7 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_628:888 0 -0 +0 NoSolution
i33C-assembly_contig_628:1-1946 log:
Finished processing i33C-assembly_contig_628:1-1946
Processing i33C-assembly_contig_729:1-520
unpaired ngmlrMAP_ONT.sorted.bam: coverage 32
Total Reads: 34, Coverage: 32, minDepth: 5
Confirmed 471 of 520 bases (90.58%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_729:1-520 log:
Finished processing i33C-assembly_contig_729:1-520
Processing i33C-assembly_contig_728:1-729
unpaired ngmlrMAP_ONT.sorted.bam: coverage 4
Total Reads: 8, Coverage: 4, minDepth: 5
Confirmed 266 of 729 bases (36.49%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_728:1-729 log:
Finished processing i33C-assembly_contig_728:1-729
Processing i33C-assembly_contig_727:1-767
unpaired ngmlrMAP_ONT.sorted.bam: coverage 31
Total Reads: 35, Coverage: 31, minDepth: 5
Confirmed 724 of 767 bases (94.39%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_727:1-767 log:
Finished processing i33C-assembly_contig_727:1-767
Processing i33C-assembly_contig_726:1-1512
unpaired ngmlrMAP_ONT.sorted.bam: coverage 41
Total Reads: 44, Coverage: 41, minDepth: 5
Confirmed 1410 of 1512 bases (93.25%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_726:1-1512 log:
Finished processing i33C-assembly_contig_726:1-1512
Processing i33C-assembly_contig_725:1-1512
unpaired ngmlrMAP_ONT.sorted.bam: coverage 36
Total Reads: 40, Coverage: 36, minDepth: 5
Confirmed 1358 of 1512 bases (89.81%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_725:1-1512 log:
Finished processing i33C-assembly_contig_725:1-1512
Processing i33C-assembly_contig_724:1-522
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 522 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_724:1-522 log:
Finished processing i33C-assembly_contig_724:1-522
Processing i33C-assembly_contig_723:1-9230
unpaired ngmlrMAP_ONT.sorted.bam: coverage 27
Total Reads: 57, Coverage: 27, minDepth: 5
Confirmed 8511 of 9230 bases (92.21%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 7 small deletions totaling 9 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_723:5069 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_723:7143 0 -0 +0 NoSolution
i33C-assembly_contig_723:1-9230 log:
Finished processing i33C-assembly_contig_723:1-9230
Processing i33C-assembly_contig_722:1-1663
unpaired ngmlrMAP_ONT.sorted.bam: coverage 51
Total Reads: 60, Coverage: 51, minDepth: 5
Confirmed 1515 of 1663 bases (91.10%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_722:1-1663 log:
Finished processing i33C-assembly_contig_722:1-1663
Processing i33C-assembly_contig_721:1-2061
unpaired ngmlrMAP_ONT.sorted.bam: coverage 5
Total Reads: 29, Coverage: 5, minDepth: 5
Confirmed 744 of 2061 bases (36.10%)
Corrected 0 snps; 0 ambiguous bases; corrected 3 small insertions totaling 5 bases, 9 small deletions totaling 38 bases
i33C-assembly_contig_721:1-2061 log:
Finished processing i33C-assembly_contig_721:1-2061
Processing i33C-assembly_contig_720:1-636
unpaired ngmlrMAP_ONT.sorted.bam: coverage 25
Total Reads: 27, Coverage: 25, minDepth: 5
Confirmed 566 of 636 bases (88.99%)
Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_720:1-636 log:
Finished processing i33C-assembly_contig_720:1-636
Processing i33C-assembly_contig_622:1-435
unpaired ngmlrMAP_ONT.sorted.bam: coverage 12
Total Reads: 21, Coverage: 12, minDepth: 5
Confirmed 306 of 435 bases (70.34%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_622:1-435 log:
Finished processing i33C-assembly_contig_622:1-435
Processing i33C-assembly_contig_623:1-545
unpaired ngmlrMAP_ONT.sorted.bam: coverage 7
Total Reads: 8, Coverage: 7, minDepth: 5
Confirmed 446 of 545 bases (81.83%)
Corrected 0 snps; 0 ambiguous bases; corrected 1 small insertions totaling 1 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_623:1-545 log:
Finished processing i33C-assembly_contig_623:1-545
Processing i33C-assembly_contig_620:1-191
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 191 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_620:1-191 log:
Finished processing i33C-assembly_contig_620:1-191
Processing i33C-assembly_contig_548:1-760
unpaired ngmlrMAP_ONT.sorted.bam: coverage 1
Total Reads: 4, Coverage: 1, minDepth: 5
Confirmed 0 of 760 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_548:1-760 log:
Finished processing i33C-assembly_contig_548:1-760
Processing i33C-assembly_contig_626:1-413
unpaired ngmlrMAP_ONT.sorted.bam: coverage 3
Total Reads: 3, Coverage: 3, minDepth: 5
Confirmed 0 of 413 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_626:1-413 log:
Finished processing i33C-assembly_contig_626:1-413
Processing i33C-assembly_contig_627:1-982
unpaired ngmlrMAP_ONT.sorted.bam: coverage 14
Total Reads: 16, Coverage: 14, minDepth: 5
Confirmed 825 of 982 bases (84.01%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_627:1-982 log:
Finished processing i33C-assembly_contig_627:1-982
Processing i33C-assembly_contig_624:1-2861
unpaired ngmlrMAP_ONT.sorted.bam: coverage 386
Total Reads: 532, Coverage: 386, minDepth: 39
Confirmed 2683 of 2861 bases (93.78%)
Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_624:1-2861 log:
Finished processing i33C-assembly_contig_624:1-2861
Processing i33C-assembly_contig_625:1-1428
unpaired ngmlrMAP_ONT.sorted.bam: coverage 33
Total Reads: 49, Coverage: 33, minDepth: 5
Confirmed 1299 of 1428 bases (90.97%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 3 bases
i33C-assembly_contig_625:1-1428 log:
Finished processing i33C-assembly_contig_625:1-1428
Processing i33C-assembly_contig_543:1-330
unpaired ngmlrMAP_ONT.sorted.bam: coverage 4
Total Reads: 5, Coverage: 4, minDepth: 5
Confirmed 108 of 330 bases (32.73%)
Corrected 0 snps; 0 ambiguous bases; corrected 1 small insertions totaling 1 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_543:1-330 log:
Finished processing i33C-assembly_contig_543:1-330
Processing i33C-assembly_contig_542:1-1529
unpaired ngmlrMAP_ONT.sorted.bam: coverage 22
Total Reads: 35, Coverage: 22, minDepth: 5
Confirmed 1347 of 1529 bases (88.10%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_542:1-1529 log:
Finished processing i33C-assembly_contig_542:1-1529
Processing i33C-assembly_contig_541:1-1367
unpaired ngmlrMAP_ONT.sorted.bam: coverage 5
Total Reads: 5, Coverage: 5, minDepth: 5
Confirmed 783 of 1367 bases (57.28%)
Corrected 1 snps; 0 ambiguous bases; corrected 8 small insertions totaling 9 bases, 9 small deletions totaling 12 bases
i33C-assembly_contig_541:1-1367 log:
Finished processing i33C-assembly_contig_541:1-1367
Processing i33C-assembly_contig_540:1-937
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 1, Coverage: 0, minDepth: 5
Confirmed 0 of 937 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_540:1-937 log:
Finished processing i33C-assembly_contig_540:1-937
Processing i33C-assembly_contig_547:1-620
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 620 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_547:1-620 log:
Finished processing i33C-assembly_contig_547:1-620
Processing i33C-assembly_contig_546:1-1197
unpaired ngmlrMAP_ONT.sorted.bam: coverage 8
Total Reads: 9, Coverage: 8, minDepth: 5
Confirmed 1036 of 1197 bases (86.55%)
Corrected 0 snps; 0 ambiguous bases; corrected 2 small insertions totaling 2 bases, 5 small deletions totaling 6 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_546:423-623 0 -0 +0 NoSolution
i33C-assembly_contig_546:1-1197 log:
Finished processing i33C-assembly_contig_546:1-1197
Processing i33C-assembly_contig_545:1-412
unpaired ngmlrMAP_ONT.sorted.bam: coverage 12
Total Reads: 13, Coverage: 12, minDepth: 5
Confirmed 343 of 412 bases (83.25%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_545:1-412 log:
Finished processing i33C-assembly_contig_545:1-412
Processing i33C-assembly_contig_544:1-538
unpaired ngmlrMAP_ONT.sorted.bam: coverage 11
Total Reads: 20, Coverage: 11, minDepth: 5
Confirmed 477 of 538 bases (88.66%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_544:1-538 log:
Finished processing i33C-assembly_contig_544:1-538
Processing i33C-assembly_contig_1036:1-819
unpaired ngmlrMAP_ONT.sorted.bam: coverage 2
Total Reads: 5, Coverage: 2, minDepth: 5
Confirmed 0 of 819 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_1036:1-819 log:
Finished processing i33C-assembly_contig_1036:1-819
Processing i33C-assembly_contig_990:1-350
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 350 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_990:1-350 log:
Finished processing i33C-assembly_contig_990:1-350
Processing i33C-assembly_contig_994:1-1989
unpaired ngmlrMAP_ONT.sorted.bam: coverage 72
Total Reads: 103, Coverage: 72, minDepth: 7
Confirmed 1884 of 1989 bases (94.72%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_994:525 0 -0 +0 NoSolution
i33C-assembly_contig_994:1-1989 log:
Finished processing i33C-assembly_contig_994:1-1989
Processing i33C-assembly_contig_858:1-3081
unpaired ngmlrMAP_ONT.sorted.bam: coverage 97
Total Reads: 129, Coverage: 97, minDepth: 10
Confirmed 2811 of 3081 bases (91.24%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 52 bases
i33C-assembly_contig_858:1-3081 log:
Finished processing i33C-assembly_contig_858:1-3081
Processing i33C-assembly_contig_1071:1-1098
unpaired ngmlrMAP_ONT.sorted.bam: coverage 50
Total Reads: 97, Coverage: 50, minDepth: 5
Confirmed 917 of 1098 bases (83.52%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_1071:1-1098 log:
Finished processing i33C-assembly_contig_1071:1-1098
Processing i33C-assembly_contig_1116:1-28302
unpaired ngmlrMAP_ONT.sorted.bam: coverage 47
Total Reads: 247, Coverage: 47, minDepth: 5
Confirmed 25358 of 28302 bases (89.60%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 16 small deletions totaling 17 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_1116:1726-1799 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1116:2959-2995 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1116:19433-19525 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1116:21118 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1116:23451 0 -0 +0 NoSolution
i33C-assembly_contig_1116:1-28302 log:
Finished processing i33C-assembly_contig_1116:1-28302
Processing i33C-assembly_contig_992:1-583
unpaired ngmlrMAP_ONT.sorted.bam: coverage 5
Total Reads: 5, Coverage: 5, minDepth: 5
Confirmed 368 of 583 bases (63.12%)
Corrected 0 snps; 0 ambiguous bases; corrected 1 small insertions totaling 2 bases, 4 small deletions totaling 8 bases
i33C-assembly_contig_992:1-583 log:
Finished processing i33C-assembly_contig_992:1-583
Processing i33C-assembly_contig_1070:1-1369
unpaired ngmlrMAP_ONT.sorted.bam: coverage 57
Total Reads: 73, Coverage: 57, minDepth: 6
Confirmed 1302 of 1369 bases (95.11%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 3 bases
i33C-assembly_contig_1070:1-1369 log:
Finished processing i33C-assembly_contig_1070:1-1369
Processing i33C-assembly_contig_938:1-793
unpaired ngmlrMAP_ONT.sorted.bam: coverage 69
Total Reads: 73, Coverage: 69, minDepth: 7
Confirmed 766 of 793 bases (96.60%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_938:1-793 log:
Finished processing i33C-assembly_contig_938:1-793
Processing i33C-assembly_contig_993:1-12973
unpaired ngmlrMAP_ONT.sorted.bam: coverage 27
Total Reads: 102, Coverage: 27, minDepth: 5
Confirmed 11105 of 12973 bases (85.60%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 5 small deletions totaling 6 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_993:4168-4870 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_993:5074 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_993:6508 0 -0 +0 NoSolution
i33C-assembly_contig_993:1-12973 log:
Finished processing i33C-assembly_contig_993:1-12973
Processing i33C-assembly_contig_1081:1-1876
unpaired ngmlrMAP_ONT.sorted.bam: coverage 11
Total Reads: 14, Coverage: 11, minDepth: 5
Confirmed 1413 of 1876 bases (75.32%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 7 small deletions totaling 158 bases
i33C-assembly_contig_1081:1-1876 log:
Finished processing i33C-assembly_contig_1081:1-1876
Processing i33C-assembly_contig_587:1-691
unpaired ngmlrMAP_ONT.sorted.bam: coverage 4
Total Reads: 8, Coverage: 4, minDepth: 5
Confirmed 275 of 691 bases (39.80%)
Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 5 bases
i33C-assembly_contig_587:1-691 log:
Finished processing i33C-assembly_contig_587:1-691
Processing i33C-assembly_contig_854:1-1517
unpaired ngmlrMAP_ONT.sorted.bam: coverage 36
Total Reads: 46, Coverage: 36, minDepth: 5
Confirmed 1408 of 1517 bases (92.81%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_854:1-1517 log:
Finished processing i33C-assembly_contig_854:1-1517
Processing i33C-assembly_contig_857:1-1260
unpaired ngmlrMAP_ONT.sorted.bam: coverage 7
Total Reads: 13, Coverage: 7, minDepth: 5
Confirmed 543 of 1260 bases (43.10%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_857:1-1260 log:
Finished processing i33C-assembly_contig_857:1-1260
Processing i33C-assembly_contig_437:1-244
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 244 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_437:1-244 log:
Finished processing i33C-assembly_contig_437:1-244
Processing i33C-assembly_contig_436:1-832
unpaired ngmlrMAP_ONT.sorted.bam: coverage 23
Total Reads: 48, Coverage: 23, minDepth: 5
Confirmed 485 of 832 bases (58.29%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 2 bases
i33C-assembly_contig_436:1-832 log:
Finished processing i33C-assembly_contig_436:1-832
Processing i33C-assembly_contig_435:1-3664
unpaired ngmlrMAP_ONT.sorted.bam: coverage 24
Total Reads: 42, Coverage: 24, minDepth: 5
Confirmed 3363 of 3664 bases (91.78%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 7 small deletions totaling 8 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_435:2602 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_435:3433 0 -0 +0 NoSolution
i33C-assembly_contig_435:1-3664 log:
Finished processing i33C-assembly_contig_435:1-3664
Processing i33C-assembly_contig_434:1-1274
unpaired ngmlrMAP_ONT.sorted.bam: coverage 40
Total Reads: 65, Coverage: 40, minDepth: 5
Confirmed 1134 of 1274 bases (89.01%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 4 small deletions totaling 6 bases
i33C-assembly_contig_434:1-1274 log:
Finished processing i33C-assembly_contig_434:1-1274
Processing i33C-assembly_contig_349:1-303
unpaired ngmlrMAP_ONT.sorted.bam: coverage 21
Total Reads: 22, Coverage: 21, minDepth: 5
Confirmed 277 of 303 bases (91.42%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_349:1-303 log:
Finished processing i33C-assembly_contig_349:1-303
Processing i33C-assembly_contig_348:1-991
unpaired ngmlrMAP_ONT.sorted.bam: coverage 1
Total Reads: 1, Coverage: 1, minDepth: 5
Confirmed 0 of 991 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_348:1-991 log:
Finished processing i33C-assembly_contig_348:1-991
Processing i33C-assembly_contig_431:1-967
unpaired ngmlrMAP_ONT.sorted.bam: coverage 7
Total Reads: 9, Coverage: 7, minDepth: 5
Confirmed 724 of 967 bases (74.87%)
Corrected 1 snps; 0 ambiguous bases; corrected 2 small insertions totaling 32 bases, 4 small deletions totaling 5 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_431:580 0 -0 +0 NoSolution
i33C-assembly_contig_431:1-967 log:
Finished processing i33C-assembly_contig_431:1-967
Processing i33C-assembly_contig_430:1-922
unpaired ngmlrMAP_ONT.sorted.bam: coverage 5
Total Reads: 7, Coverage: 5, minDepth: 5
Confirmed 254 of 922 bases (27.55%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_430:1-922 log:
Finished processing i33C-assembly_contig_430:1-922
Processing i33C-assembly_contig_345:1-2106
unpaired ngmlrMAP_ONT.sorted.bam: coverage 19
Total Reads: 48, Coverage: 19, minDepth: 5
Confirmed 1748 of 2106 bases (83.00%)
Corrected 1 snps; 0 ambiguous bases; corrected 1 small insertions totaling 40 bases, 5 small deletions totaling 6 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_345:1627-1744 0 -0 +0 NoSolution
i33C-assembly_contig_345:1-2106 log:
Finished processing i33C-assembly_contig_345:1-2106
Processing i33C-assembly_contig_344:1-943
unpaired ngmlrMAP_ONT.sorted.bam: coverage 13
Total Reads: 27, Coverage: 13, minDepth: 5
Confirmed 780 of 943 bases (82.71%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_344:1-943 log:
Finished processing i33C-assembly_contig_344:1-943
Processing i33C-assembly_contig_347:1-1193
unpaired ngmlrMAP_ONT.sorted.bam: coverage 19
Total Reads: 20, Coverage: 19, minDepth: 5
Confirmed 1080 of 1193 bases (90.53%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_347:1-1193 log:
Finished processing i33C-assembly_contig_347:1-1193
Processing i33C-assembly_contig_346:1-813
unpaired ngmlrMAP_ONT.sorted.bam: coverage 21
Total Reads: 23, Coverage: 21, minDepth: 5
Confirmed 721 of 813 bases (88.68%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_346:1-813 log:
Finished processing i33C-assembly_contig_346:1-813
Processing i33C-assembly_contig_341:1-1039
unpaired ngmlrMAP_ONT.sorted.bam: coverage 1
Total Reads: 3, Coverage: 1, minDepth: 5
Confirmed 0 of 1039 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_341:1-1039 log:
Finished processing i33C-assembly_contig_341:1-1039
Processing i33C-assembly_contig_340:1-1039
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 1, Coverage: 0, minDepth: 5
Confirmed 0 of 1039 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_340:1-1039 log:
Finished processing i33C-assembly_contig_340:1-1039
Processing i33C-assembly_contig_343:1-83
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 83 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_343:1-83 log:
Finished processing i33C-assembly_contig_343:1-83
Processing i33C-assembly_contig_342:1-4207
unpaired ngmlrMAP_ONT.sorted.bam: coverage 26
Total Reads: 57, Coverage: 26, minDepth: 5
Confirmed 3676 of 4207 bases (87.38%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 9 small deletions totaling 11 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_342:2586-2587 0 -0 +0 NoSolution
i33C-assembly_contig_342:1-4207 log:
Finished processing i33C-assembly_contig_342:1-4207
Processing i33C-assembly_contig_262:1-228
unpaired ngmlrMAP_ONT.sorted.bam: coverage 7
Total Reads: 9, Coverage: 7, minDepth: 5
Confirmed 147 of 228 bases (64.47%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_262:1-228 log:
Finished processing i33C-assembly_contig_262:1-228
Processing i33C-assembly_contig_263:1-965
unpaired ngmlrMAP_ONT.sorted.bam: coverage 4
Total Reads: 4, Coverage: 4, minDepth: 5
Confirmed 15 of 965 bases (1.55%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_263:1-965 log:
Finished processing i33C-assembly_contig_263:1-965
Processing i33C-assembly_contig_189:1-165
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 165 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_189:1-165 log:
Finished processing i33C-assembly_contig_189:1-165
Processing i33C-assembly_contig_188:1-710
unpaired ngmlrMAP_ONT.sorted.bam: coverage 29
Total Reads: 43, Coverage: 29, minDepth: 5
Confirmed 666 of 710 bases (93.80%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_188:1-710 log:
Finished processing i33C-assembly_contig_188:1-710
Processing i33C-assembly_contig_266:1-4976
unpaired ngmlrMAP_ONT.sorted.bam: coverage 21
Total Reads: 53, Coverage: 21, minDepth: 5
Confirmed 3851 of 4976 bases (77.39%)
Corrected 133 snps; 6 ambiguous bases; corrected 14 small insertions totaling 16 bases, 20 small deletions totaling 24 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_266:624-679 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_266:3428-3951 0 -0 +0 NoSolution
i33C-assembly_contig_266:1-4976 log:
Finished processing i33C-assembly_contig_266:1-4976
Processing i33C-assembly_contig_267:1-962
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 962 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_267:1-962 log:
Finished processing i33C-assembly_contig_267:1-962
Processing i33C-assembly_contig_264:1-1213
unpaired ngmlrMAP_ONT.sorted.bam: coverage 23
Total Reads: 31, Coverage: 23, minDepth: 5
Confirmed 1092 of 1213 bases (90.02%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 4 bases
i33C-assembly_contig_264:1-1213 log:
Finished processing i33C-assembly_contig_264:1-1213
Processing i33C-assembly_contig_265:1-962
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 962 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_265:1-962 log:
Finished processing i33C-assembly_contig_265:1-962
Processing i33C-assembly_contig_183:1-1475
unpaired ngmlrMAP_ONT.sorted.bam: coverage 133
Total Reads: 153, Coverage: 133, minDepth: 13
Confirmed 1393 of 1475 bases (94.44%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_183:1-1475 log:
Finished processing i33C-assembly_contig_183:1-1475
Processing i33C-assembly_contig_182:1-2093
unpaired ngmlrMAP_ONT.sorted.bam: coverage 9
Total Reads: 19, Coverage: 9, minDepth: 5
Confirmed 1496 of 2093 bases (71.48%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 7 small deletions totaling 11 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_182:1011 0 -0 +0 NoSolution
i33C-assembly_contig_182:1-2093 log:
Finished processing i33C-assembly_contig_182:1-2093
Processing i33C-assembly_contig_181:1-1396
unpaired ngmlrMAP_ONT.sorted.bam: coverage 42
Total Reads: 48, Coverage: 42, minDepth: 5
Confirmed 1256 of 1396 bases (89.97%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 2 bases
i33C-assembly_contig_181:1-1396 log:
Finished processing i33C-assembly_contig_181:1-1396
Processing i33C-assembly_contig_180:1-1554
unpaired ngmlrMAP_ONT.sorted.bam: coverage 44
Total Reads: 53, Coverage: 44, minDepth: 5
Confirmed 1463 of 1554 bases (94.14%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_180:1-1554 log:
Finished processing i33C-assembly_contig_180:1-1554
Processing i33C-assembly_contig_187:1-1262
unpaired ngmlrMAP_ONT.sorted.bam: coverage 32
Total Reads: 48, Coverage: 32, minDepth: 5
Confirmed 1128 of 1262 bases (89.38%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_187:1-1262 log:
Finished processing i33C-assembly_contig_187:1-1262
Processing i33C-assembly_contig_186:1-1296
unpaired ngmlrMAP_ONT.sorted.bam: coverage 1
Total Reads: 4, Coverage: 1, minDepth: 5
Confirmed 0 of 1296 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_186:1-1296 log:
Finished processing i33C-assembly_contig_186:1-1296
Processing i33C-assembly_contig_185:1-1011
unpaired ngmlrMAP_ONT.sorted.bam: coverage 2
Total Reads: 3, Coverage: 2, minDepth: 5
Confirmed 0 of 1011 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_185:1-1011 log:
Finished processing i33C-assembly_contig_185:1-1011
Processing i33C-assembly_contig_184:1-147
unpaired ngmlrMAP_ONT.sorted.bam: coverage 1
Total Reads: 1, Coverage: 1, minDepth: 5
Confirmed 0 of 147 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_184:1-147 log:
Finished processing i33C-assembly_contig_184:1-147
Processing i33C-assembly_contig_947:1-1583
unpaired ngmlrMAP_ONT.sorted.bam: coverage 24
Total Reads: 28, Coverage: 24, minDepth: 5
Confirmed 1443 of 1583 bases (91.16%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 4 bases
i33C-assembly_contig_947:1-1583 log:
Finished processing i33C-assembly_contig_947:1-1583
Processing i33C-assembly_contig_946:1-2067
unpaired ngmlrMAP_ONT.sorted.bam: coverage 68
Total Reads: 84, Coverage: 68, minDepth: 7
Confirmed 1929 of 2067 bases (93.32%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 2 bases
i33C-assembly_contig_946:1-2067 log:
Finished processing i33C-assembly_contig_946:1-2067
Processing i33C-assembly_contig_945:1-1243
unpaired ngmlrMAP_ONT.sorted.bam: coverage 39
Total Reads: 82, Coverage: 39, minDepth: 5
Confirmed 1049 of 1243 bases (84.39%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_945:997 0 -0 +0 NoSolution
i33C-assembly_contig_945:1-1243 log:
Finished processing i33C-assembly_contig_945:1-1243
Processing i33C-assembly_contig_944:1-1335
unpaired ngmlrMAP_ONT.sorted.bam: coverage 106
Total Reads: 198, Coverage: 106, minDepth: 11
Confirmed 1261 of 1335 bases (94.46%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 2 bases
i33C-assembly_contig_944:1-1335 log:
Finished processing i33C-assembly_contig_944:1-1335
Processing i33C-assembly_contig_943:1-419
unpaired ngmlrMAP_ONT.sorted.bam: coverage 25
Total Reads: 27, Coverage: 25, minDepth: 5
Confirmed 383 of 419 bases (91.41%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
i33C-assembly_contig_943:1-419 log:
Finished processing i33C-assembly_contig_943:1-419
Processing i33C-assembly_contig_829:1-9553
unpaired ngmlrMAP_ONT.sorted.bam: coverage 37
Total Reads: 81, Coverage: 37, minDepth: 5
Confirmed 8840 of 9553 bases (92.54%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 6 small deletions totaling 6 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_829:2680 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_829:7514 0 -0 +0 NoSolution
i33C-assembly_contig_829:1-9553 log:
Finished processing i33C-assembly_contig_829:1-9553
Processing i33C-assembly_contig_941:1-1052
unpaired ngmlrMAP_ONT.sorted.bam: coverage 4
Total Reads: 4, Coverage: 4, minDepth: 5
Confirmed 1 of 1052 bases (0.10%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_941:1-1052 log:
Finished processing i33C-assembly_contig_941:1-1052
Processing i33C-assembly_contig_539:1-1529
unpaired ngmlrMAP_ONT.sorted.bam: coverage 7
Total Reads: 15, Coverage: 7, minDepth: 5
Confirmed 1134 of 1529 bases (74.17%)
Corrected 1 snps; 1 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 3 bases
i33C-assembly_contig_539:1-1529 log:
Finished processing i33C-assembly_contig_539:1-1529
Processing i33C-assembly_contig_536:1-1821
unpaired ngmlrMAP_ONT.sorted.bam: coverage 597
Total Reads: 718, Coverage: 597, minDepth: 60
Confirmed 1719 of 1821 bases (94.40%)
Corrected 5 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_536:1-1821 log:
Finished processing i33C-assembly_contig_536:1-1821
Processing i33C-assembly_contig_537:1-538
unpaired ngmlrMAP_ONT.sorted.bam: coverage 21
Total Reads: 33, Coverage: 21, minDepth: 5
Confirmed 478 of 538 bases (88.85%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_537:1-538 log:
Finished processing i33C-assembly_contig_537:1-538
Processing i33C-assembly_contig_826:1-12097
unpaired ngmlrMAP_ONT.sorted.bam: coverage 29
Total Reads: 88, Coverage: 29, minDepth: 5
Confirmed 11095 of 12097 bases (91.72%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 13 small deletions totaling 14 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_826:9282 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_826:9847 0 -0 +0 NoSolution
i33C-assembly_contig_826:1-12097 log:
Finished processing i33C-assembly_contig_826:1-12097
Processing i33C-assembly_contig_535:1-1220
unpaired ngmlrMAP_ONT.sorted.bam: coverage 43
Total Reads: 61, Coverage: 43, minDepth: 5
Confirmed 1125 of 1220 bases (92.21%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_535:310 0 -0 +0 NoSolution
i33C-assembly_contig_535:1-1220 log:
Finished processing i33C-assembly_contig_535:1-1220
Processing i33C-assembly_contig_532:1-51959
unpaired ngmlrMAP_ONT.sorted.bam: coverage 11
Total Reads: 126, Coverage: 11, minDepth: 5
Confirmed 30937 of 51959 bases (59.54%)
Corrected 5 snps; 0 ambiguous bases; corrected 7 small insertions totaling 9 bases, 70 small deletions totaling 214 bases
Large collapsed region: i33C-assembly_contig_532:29980-44647 size 14668
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_532:875-908 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:1274-1351 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:2219 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:3931-11588 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:11868-12585 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:12816-14819 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:15083-15196 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:15771 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:17819 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:19474-19502 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:19794-24552 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:28718-28780 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:30196 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:32097-32225 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:35666 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:35898 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:38068-38103 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:40658 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:40976-40977 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:42121 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:44473-44474 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:47364 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:48007 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:48359 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_532:49642 0 -0 +0 NoSolution
i33C-assembly_contig_532:1-51959 log:
Finished processing i33C-assembly_contig_532:1-51959
Processing i33C-assembly_contig_821:1-150
unpaired ngmlrMAP_ONT.sorted.bam: coverage 10
Total Reads: 11, Coverage: 10, minDepth: 5
Confirmed 123 of 150 bases (82.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_821:1-150 log:
Finished processing i33C-assembly_contig_821:1-150
Processing i33C-assembly_contig_530:1-2440
unpaired ngmlrMAP_ONT.sorted.bam: coverage 93
Total Reads: 147, Coverage: 93, minDepth: 9
Confirmed 2249 of 2440 bases (92.17%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 3 bases
i33C-assembly_contig_530:1-2440 log:
Finished processing i33C-assembly_contig_530:1-2440
Processing i33C-assembly_contig_531:1-811
unpaired ngmlrMAP_ONT.sorted.bam: coverage 0
Total Reads: 1, Coverage: 0, minDepth: 5
Confirmed 0 of 811 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_531:1-811 log:
Finished processing i33C-assembly_contig_531:1-811
Processing i33C-assembly_contig_449:1-878
unpaired ngmlrMAP_ONT.sorted.bam: coverage 87
Total Reads: 151, Coverage: 87, minDepth: 9
Confirmed 818 of 878 bases (93.17%)
Corrected 7 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
i33C-assembly_contig_449:1-878 log:
Finished processing i33C-assembly_contig_449:1-878
Processing i33C-assembly_contig_1084:1-712
unpaired ngmlrMAP_ONT.sorted.bam: coverage 5
Total Reads: 5, Coverage: 5, minDepth: 5
Confirmed 545 of 712 bases (76.54%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 2 small deletions totaling 4 bases
i33C-assembly_contig_1084:1-712 log:
Finished processing i33C-assembly_contig_1084:1-712
Processing i33C-assembly_contig_1127:1-8076670
unpaired ngmlrMAP_ONT.sorted.bam: coverage 62
Total Reads: 76049, Coverage: 62, minDepth: 6
Confirmed 7581872 of 8076670 bases (93.87%)
Corrected 113 snps; 10 ambiguous bases; corrected 47 small insertions totaling 4767 bases, 4742 small deletions totaling 28141 bases
Large collapsed region: i33C-assembly_contig_1127:885636-898178 size 12543
# Attempting to fix local continuity breaks
# fix break: i33C-assembly_contig_1127:23130-25395 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:25829 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:26799-29571 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:30127 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:30346-30369 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:30618-30625 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:31028 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:31289-31355 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:31714-31940 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:32828 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:33037-54201 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:54478 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:55116-55135 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:55553-59741 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:60002 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:60374-60814 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:61387 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:62196-62308 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:62794-62797 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:66099 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:71318-71319 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:72781-72832 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:73094 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:77821 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:79361 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:82392-82393 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:89050 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:92631 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:105584 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:108379-108521 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:117137 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:118789-118790 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:119296-120556 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:120889-120895 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:121113-121569 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:122947-126693 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:126974 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:127209-127248 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:127474-127803 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:128189-144832 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:145291 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:145506 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:147370-157996 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:159763-180309 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:180685 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:181072-181178 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:181945 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:182630-182799 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:185800-186053 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:186331-191048 0 -0 +0 NoSolution
fix break: i33C-assembly_contig_1127:193795-193806 193795 -102 +585 OpenedGap
# fix break: i33C-assembly_contig_1127:194778-194839 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:195370-199016 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:199240-214163 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:214583-216967 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:217187-227632 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:228162-228456 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:228725-228838 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:229076-242290 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:243257-260594 0 -0 +0 NoSolution
# fix break: i33C-assembly_contig_1127:261744-261943 0 -0 +0 NoSolution
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.simontuffs.onejar.Boot.run(Boot.java:340)
    at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.lang.String.substring(String.java:1969)
    at scala.collection.immutable.StringOps$.slice$extension(StringOps.scala:44)
    at org.broadinstitute.pilon.Assembler$$anonfun$addToPileups$1.apply$mcVI$sp(Assembler.scala:82)
    at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160)
    at org.broadinstitute.pilon.Assembler.addToPileups(Assembler.scala:81)
    at org.broadinstitute.pilon.Assembler.addRead(Assembler.scala:66)
    at org.broadinstitute.pilon.Assembler$$anonfun$addReads$1.apply(Assembler.scala:48)
    at org.broadinstitute.pilon.Assembler$$anonfun$addReads$1.apply(Assembler.scala:48)
    at scala.collection.immutable.List.foreach(List.scala:381)
    at org.broadinstitute.pilon.Assembler.addReads(Assembler.scala:48)
    at org.broadinstitute.pilon.GapFiller.assembleIntoBreak(GapFiller.scala:124)
    at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:52)
    at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:45)
    at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:383)
    at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:381)
    at scala.collection.immutable.List.foreach(List.scala:381)
    at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:381)
    at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:119)
    at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:108)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    at scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
    at scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969)
    at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
    at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
    at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
    at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)