RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.H7gGKo/RM_1176595.MonAug250805102025 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: 1756134310 Database = /dev/shm/rModeler.H7gGKo/GCA_025311615.1_ASM2531161v1 - Sequences = 12429 - Bases = 1097572847 - N50 = 35153587 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48432096-51891496 | [ 2 ] 44972696-48432095 | [ 1 ] 41513296-44972695 | [ 5 ] 38053897-41513296 | [ 2 ] 34594497-38053896 | [ 3 ] 31135097-34594496 | [ 2 ] 27675697-31135096 | [ 4 ] 24216298-27675697 | [ 4 ] 20756898-24216297 | [ 6 ] 17297498-20756897 | [ 5 ] 13838098-17297497 | [ 1 ] 10378699-13838098 | [ ] 6919299-10378698 | [ ] 3459899-6919298 | [ ] 500-3459899 |************************************************** [ 12394 ] Storage Throughput = excellent ( 1115.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 95207589 bp ( 40008066 non ambiguous ) - Num Contigs Represented = 1138 - Sequence extraction : 00:04:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:23 (hh:mm:ss) Elapsed Time Round Time: 00:13:41 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2337 repeats masked totaling 342249 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 24084996 bp Num Contigs Represented = 324 Non ambiguous bp: Initial: 10008836 bp After Masking: 9638908 bp Masked: 3.70 % -- Input Database Coverage: 24084996 bp out of 1097572847 bp ( 2.19 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 388521 Comparison Time: 00:12:22 (hh:mm:ss) Elapsed Time, 1357 HSPs Collected Number of families returned by RECON: 436 Round Time: 00:13:57 (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 : 00:03:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7055 repeats masked totaling 1012210 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 71162532 bp Num Contigs Represented = 851 Non ambiguous bp: Initial: 30021729 bp After Masking: 28907801 bp Masked: 3.71 % -- Input Database Coverage: 95247528 bp out of 1097572847 bp ( 8.68 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3319176 Comparison Time: 01:10:33 (hh:mm:ss) Elapsed Time, 11827 HSPs Collected Number of families returned by RECON: 2395 Round Time: 01:15:22 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23634 repeats masked totaling 3493524 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 215653426 bp Num Contigs Represented = 2444 Non ambiguous bp: Initial: 90019648 bp After Masking: 86235278 bp Masked: 4.20 % -- Input Database Coverage: 310900954 bp out of 1097572847 bp ( 28.33 % ) Sampling Time: 00:13:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29980896 Comparison Time: 08:46:09 (hh:mm:ss) Elapsed Time, 56314 HSPs Collected Number of families returned by RECON: 14098 Round Time: 09:03:40 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86749 repeats masked totaling 13329606 bp(s). - TE Masking time 00:03:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 643732506 bp Num Contigs Represented = 7335 Non ambiguous bp: Initial: 270009353 bp After Masking: 255794334 bp Masked: 5.26 % -- Input Database Coverage: 954633460 bp out of 1097572847 bp ( 86.98 % ) Sampling Time: 00:39:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 270083661 Comparison Time: 72:29:21 (hh:mm:ss) Elapsed Time, 268616 HSPs Collected Number of families returned by RECON: 90395 Round Time: 75:05:58 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatScout/RECON discovery complete: 638 families found Classification Time: 00:19:17 (hh:mm:ss) Elapsed Time Program Time: 86:11:55 (hh:mm:ss) Elapsed Time