RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.jB1oN0/RM_3734797.SatNov160327062024 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: 1731756424 Database = /scratch/tmp/rModeler.jB1oN0/GCA_041834305.1_ASM4183430v1 - Sequences = 1355 - Bases = 3146604256 - N50 = 108253378 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 178788577-191558633 | [ 3 ] 166018521-178788576 | [ ] 153248466-166018521 | [ ] 140478410-153248465 | [ 2 ] 127708355-140478410 | [ 1 ] 114938299-127708354 | [ 3 ] 102168244-114938299 | [ 3 ] 89398188-102168243 | [ 4 ] 76628133-89398188 | [ 3 ] 63858077-76628132 | [ 1 ] 51088022-63858077 | [ 1 ] 38317966-51088021 | [ ] 25547911-38317966 | [ 1 ] 12777855-25547910 | [ 1 ] 7800-12777855 |************************************************** [ 1332 ] Storage Throughput = excellent ( 1340.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028695 bp ( 40028695 non ambiguous ) - Num Contigs Represented = 188 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:04 (hh:mm:ss) Elapsed Time Round Time: 00:16:25 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8883 repeats masked totaling 2810565 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034286 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 10034286 bp After Masking: 6441478 bp Masked: 35.81 % -- Input Database Coverage: 10034286 bp out of 3146604256 bp ( 0.32 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:30 (hh:mm:ss) Elapsed Time, 340611 HSPs Collected Number of families returned by RECON: 691 Round Time: 00:09:36 (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 : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30064 repeats masked totaling 10444834 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034334 bp Num Contigs Represented = 157 Non ambiguous bp: Initial: 30034334 bp After Masking: 17389159 bp Masked: 42.10 % -- Input Database Coverage: 40068620 bp out of 3146604256 bp ( 1.27 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:11:53 (hh:mm:ss) Elapsed Time, 77502 HSPs Collected Number of families returned by RECON: 1965 Round Time: 00:14:51 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100529 repeats masked totaling 34314861 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015607 bp Num Contigs Represented = 341 Non ambiguous bp: Initial: 90015507 bp After Masking: 48627753 bp Masked: 45.98 % -- Input Database Coverage: 130084227 bp out of 3146604256 bp ( 4.13 % ) Sampling Time: 00:07:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 00:57:59 (hh:mm:ss) Elapsed Time, 463998 HSPs Collected Number of families returned by RECON: 6466 Round Time: 01:08:34 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 332639 repeats masked totaling 108838072 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019609 bp Num Contigs Represented = 593 Non ambiguous bp: Initial: 270018709 bp After Masking: 139840177 bp Masked: 48.21 % -- Input Database Coverage: 400103836 bp out of 3146604256 bp ( 12.72 % ) Sampling Time: 00:23:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23198266 Comparison Time: 06:56:17 (hh:mm:ss) Elapsed Time, 3930793 HSPs Collected Number of families returned by RECON: 26958 Round Time: 07:31:09 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatScout/RECON discovery complete: 756 families found Classification Time: 00:19:22 (hh:mm:ss) Elapsed Time Program Time: 09:39:57 (hh:mm:ss) Elapsed Time