RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.9dZpNe/RM_1482078.SunApr132051412025 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: 1744602701 Database = /data/tmp/rModeler.9dZpNe/GCA_045345405.1_bGuaGua1_haplotype_1 - Sequences = 216 - Bases = 1366127126 - N50 = 127465315 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 157531718-168782984 | [ 2 ] 146280452-157531717 | [ ] 135029187-146280452 | [ ] 123777921-135029186 | [ 2 ] 112526656-123777921 | [ ] 101275390-112526655 | [ 1 ] 90024124-101275389 | [ 2 ] 78772859-90024124 | [ ] 67521593-78772858 | [ 1 ] 56270328-67521593 | [ ] 45019062-56270327 | [ ] 33767796-45019061 | [ 2 ] 22516531-33767796 | [ 3 ] 11265265-22516530 |* [ 6 ] 14000-11265265 |************************************************** [ 197 ] Storage Throughput = excellent ( 1288.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039206 bp ( 40038606 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:46 (hh:mm:ss) Elapsed Time Round Time: 00:26:49 (hh:mm:ss) Elapsed Time : 106 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 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4106 repeats masked totaling 1186992 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010302 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10010302 bp After Masking: 7556023 bp Masked: 24.52 % -- Input Database Coverage: 10010302 bp out of 1366127126 bp ( 0.73 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:07 (hh:mm:ss) Elapsed Time, 524 HSPs Collected Number of families returned by RECON: 179 Round Time: 00:07:48 (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 : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13129 repeats masked totaling 3486503 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028824 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30028224 bp After Masking: 22526265 bp Masked: 24.98 % -- Input Database Coverage: 40039126 bp out of 1366127126 bp ( 2.93 % ) Sampling Time: 00:05:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:26:36 (hh:mm:ss) Elapsed Time, 9198 HSPs Collected Number of families returned by RECON: 927 Round Time: 00:34:54 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40308 repeats masked totaling 11199654 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035832 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 90033432 bp After Masking: 68776289 bp Masked: 23.61 % -- Input Database Coverage: 130074958 bp out of 1366127126 bp ( 9.52 % ) Sampling Time: 00:12:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:59:09 (hh:mm:ss) Elapsed Time, 40888 HSPs Collected Number of families returned by RECON: 6441 Round Time: 03:17:32 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127783 repeats masked totaling 36919783 bp(s). - TE Masking time 00:03:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030522 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270023922 bp After Masking: 202322141 bp Masked: 25.07 % -- Input Database Coverage: 400105480 bp out of 1366127126 bp ( 29.29 % ) Sampling Time: 00:44:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 22:44:25 (hh:mm:ss) Elapsed Time, 207079 HSPs Collected Number of families returned by RECON: 42547 Round Time: 24:34:08 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatScout/RECON discovery complete: 413 families found Classification Time: 00:48:49 (hh:mm:ss) Elapsed Time Program Time: 29:50:00 (hh:mm:ss) Elapsed Time