RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oeBb34/RM_476.MonJun241503032024 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: 1719266582 Database = /dev/shm/rModeler.oeBb34/GCF_028858725.1_bColStr4.1.hap1 - Sequences = 191 - Bases = 1212482152 - N50 = 97552025 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 192816910-206588619 | [ 1 ] 179045201-192816909 | [ ] 165273493-179045201 | [ ] 151501784-165273492 | [ ] 137730076-151501784 | [ ] 123958367-137730075 | [ ] 110186658-123958366 | [ 1 ] 96414950-110186658 | [ 2 ] 82643241-96414949 | [ 1 ] 68871533-82643241 | [ ] 55099824-68871532 | [ 1 ] 41328115-55099823 | [ 3 ] 27556407-41328115 |* [ 5 ] 13784698-27556406 |* [ 5 ] 12990-13784698 |************************************************** [ 172 ] Storage Throughput = excellent ( 1169.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40121276 bp ( 40001629 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:29 (hh:mm:ss) Elapsed Time Round Time: 00:30:42 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3671 repeats masked totaling 1277556 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003057 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10002857 bp After Masking: 8412303 bp Masked: 15.90 % -- Input Database Coverage: 10003057 bp out of 1212482152 bp ( 0.83 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:26 (hh:mm:ss) Elapsed Time, 740 HSPs Collected Number of families returned by RECON: 227 Round Time: 00:06:39 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11126 repeats masked totaling 3758756 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30158060 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30038613 bp After Masking: 25508590 bp Masked: 15.08 % -- Input Database Coverage: 40161117 bp out of 1212482152 bp ( 3.31 % ) Sampling Time: 00:03:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:32:38 (hh:mm:ss) Elapsed Time, 3626 HSPs Collected Number of families returned by RECON: 1250 Round Time: 00:36:22 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33919 repeats masked totaling 11528535 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90238650 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90015934 bp After Masking: 75988293 bp Masked: 15.58 % -- Input Database Coverage: 130399767 bp out of 1212482152 bp ( 10.75 % ) Sampling Time: 00:09:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:06:30 (hh:mm:ss) Elapsed Time, 45114 HSPs Collected Number of families returned by RECON: 7649 Round Time: 04:18:34 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108975 repeats masked totaling 36401162 bp(s). - TE Masking time 00:04:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271199750 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 270031975 bp After Masking: 225364156 bp Masked: 16.54 % -- Input Database Coverage: 401599517 bp out of 1212482152 bp ( 33.12 % ) Sampling Time: 00:30:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 33:40:33 (hh:mm:ss) Elapsed Time, 205112 HSPs Collected Number of families returned by RECON: 56182 Round Time: 35:09:21 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatScout/RECON discovery complete: 436 families found Classification Time: 00:48:10 (hh:mm:ss) Elapsed Time Program Time: 41:29:48 (hh:mm:ss) Elapsed Time