RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gliGXD/RM_27836.SunDec30511072023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1701609065 Database = /dev/shm/rModeler.gliGXD/GCA_030684295.1_sSteTig4.hap2 - Sequences = 933 - Bases = 3603936669 - N50 = 75216339 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 181703178-194680986 | [ 1 ] 168725371-181703178 | [ ] 155747564-168725371 | [ 1 ] 142769756-155747563 | [ 1 ] 129791949-142769756 | [ 1 ] 116814142-129791949 | [ ] 103836334-116814141 | [ 3 ] 90858527-103836334 | [ 3 ] 77880720-90858527 | [ 3 ] 64902912-77880719 | [ 4 ] 51925105-64902912 | [ 9 ] 38947298-51925105 | [ 8 ] 25969490-38947297 | [ 5 ] 12991683-25969490 | [ 8 ] 13876-12991683 |************************************************** [ 886 ] Storage Throughput = excellent ( 1227.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40194760 bp ( 40011466 non ambiguous ) - Num Contigs Represented = 157 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:12 (hh:mm:ss) Elapsed Time Round Time: 00:37:19 (hh:mm:ss) Elapsed Time : 314 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15323 repeats masked totaling 3942778 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10079081 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10018517 bp After Masking: 4080554 bp Masked: 59.27 % -- Input Database Coverage: 10079081 bp out of 3603936669 bp ( 0.28 % ) Sampling Time: 00:11:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 5048 HSPs Collected Number of families returned by RECON: 730 Round Time: 00:16:24 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53042 repeats masked totaling 13222823 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30155524 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 30032794 bp After Masking: 11869134 bp Masked: 60.48 % -- Input Database Coverage: 40234605 bp out of 3603936669 bp ( 1.12 % ) Sampling Time: 00:27:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:20:39 (hh:mm:ss) Elapsed Time, 25027 HSPs Collected Number of families returned by RECON: 2108 Round Time: 00:49:24 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:28:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164454 repeats masked totaling 40597189 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90220051 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 90006182 bp After Masking: 32491025 bp Masked: 63.90 % -- Input Database Coverage: 130454656 bp out of 3603936669 bp ( 3.62 % ) Sampling Time: 01:34:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:59:52 (hh:mm:ss) Elapsed Time, 83329 HSPs Collected Number of families returned by RECON: 5813 Round Time: 03:43:30 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:09:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 537718 repeats masked totaling 131173086 bp(s). - TE Masking time 00:10:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270784760 bp Num Contigs Represented = 386 Non ambiguous bp: Initial: 270022971 bp After Masking: 90718713 bp Masked: 66.40 % -- Input Database Coverage: 401239416 bp out of 3603936669 bp ( 11.13 % ) Sampling Time: 04:30:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 13:03:59 (hh:mm:ss) Elapsed Time, 280471 HSPs Collected Number of families returned by RECON: 18026 Round Time: 17:53:00 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatScout/RECON discovery complete: 1203 families found Classification Time: 01:02:58 (hh:mm:ss) Elapsed Time Program Time: 24:22:35 (hh:mm:ss) Elapsed Time