RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.74HAL5/RM_716222.FriAug151122182025 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: 1755282136 Database = /data/tmp/rModeler.74HAL5/GCA_034698045.1_ASM3469804v1 - Sequences = 195691 - Bases = 275088138 - N50 = 6203 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 104962-112446 | [ 1 ] 97479-104962 | [ ] 89996-97479 | [ 2 ] 82513-89996 | [ 2 ] 75030-82513 | [ 2 ] 67547-75030 | [ 4 ] 60064-67547 | [ 7 ] 52581-60064 | [ 18 ] 45098-52581 | [ 39 ] 37615-45098 | [ 79 ] 30132-37615 | [ 203 ] 22649-30132 | [ 560 ] 15166-22649 | [ 1650 ] 7683-15166 |* [ 5776 ] 200-7683 |************************************************** [ 187348 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = fair ( 597.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013875 bp ( 40013875 non ambiguous ) - Num Contigs Represented = 28134 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:23 (hh:mm:ss) Elapsed Time Round Time: 00:16:20 (hh:mm:ss) Elapsed Time : 511 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5205 repeats masked totaling 748010 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000524 bp Num Contigs Represented = 7105 Non ambiguous bp: Initial: 10000524 bp After Masking: 9184752 bp Masked: 8.16 % -- Input Database Coverage: 10000524 bp out of 275088138 bp ( 3.64 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25236960 Comparison Time: 00:28:14 (hh:mm:ss) Elapsed Time, 5916 HSPs Collected Number of families returned by RECON: 1678 Round Time: 00:29:49 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16126 repeats masked totaling 2332737 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013272 bp Num Contigs Represented = 21031 Non ambiguous bp: Initial: 30013272 bp After Masking: 27499483 bp Masked: 8.38 % -- Input Database Coverage: 40013796 bp out of 275088138 bp ( 14.55 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 221204061 Comparison Time: 01:30:48 (hh:mm:ss) Elapsed Time, 46936 HSPs Collected Number of families returned by RECON: 7701 Round Time: 01:39:45 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50675 repeats masked totaling 7803389 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90000178 bp Num Contigs Represented = 64864 Non ambiguous bp: Initial: 90000178 bp After Masking: 81617282 bp Masked: 9.31 % -- Input Database Coverage: 130013974 bp out of 275088138 bp ( 47.26 % ) Sampling Time: 00:03:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2104350375 Comparison Time: 06:20:19 (hh:mm:ss) Elapsed Time, 366188 HSPs Collected Number of families returned by RECON: 30249 Round Time: 07:29:48 (hh:mm:ss) Elapsed Time : 485 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108196 repeats masked totaling 19745630 bp(s). - TE Masking time 00:04:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 145073908 bp Num Contigs Represented = 102758 Non ambiguous bp: Initial: 145073908 bp After Masking: 124413214 bp Masked: 14.24 % -- Input Database Coverage: 275087882 bp out of 275088138 bp ( 100.00 % ) Sampling Time: 00:08:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5283251821 Comparison Time: 12:59:40 (hh:mm:ss) Elapsed Time, 482985 HSPs Collected Number of families returned by RECON: 51501 Round Time: 15:04:46 (hh:mm:ss) Elapsed Time : 460 families discovered. RepeatScout/RECON discovery complete: 1525 families found Classification Time: 00:57:50 (hh:mm:ss) Elapsed Time Program Time: 25:58:18 (hh:mm:ss) Elapsed Time