RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nNnYq5/RM_31901.MonNov270936512023 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: 1701106611 Database = /dev/shm/rModeler.nNnYq5/GCA_027409185.1_mCynVol1.pri - Sequences = 131 - Bases = 2814434834 - N50 = 167399654 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 284174918-304471933 | [ 1 ] 263877903-284174917 | [ ] 243580889-263877903 | [ ] 223283874-243580888 | [ 1 ] 202986860-223283874 | [ ] 182689845-202986859 | [ 1 ] 162392830-182689844 |** [ 5 ] 142095816-162392830 | [ 2 ] 121798801-142095815 | [ 2 ] 101501787-121798801 |* [ 3 ] 81204772-101501786 | [ 1 ] 60907757-81204771 | [ 1 ] 40610743-60907757 | [ 1 ] 20313728-40610742 | [ ] 16714-20313728 |************************************************** [ 113 ] Storage Throughput = excellent ( 1178.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027326 bp ( 40026826 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:05 (hh:mm:ss) Elapsed Time Round Time: 00:37:49 (hh:mm:ss) Elapsed Time : 266 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9843 repeats masked totaling 2806712 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001640 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001140 bp After Masking: 6873804 bp Masked: 31.27 % -- Input Database Coverage: 10001640 bp out of 2814434834 bp ( 0.36 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 6957 HSPs Collected Number of families returned by RECON: 1020 Round Time: 00:07:58 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33206 repeats masked totaling 9011276 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025606 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30025606 bp After Masking: 19865780 bp Masked: 33.84 % -- Input Database Coverage: 40027246 bp out of 2814434834 bp ( 1.42 % ) Sampling Time: 00:05:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:39 (hh:mm:ss) Elapsed Time, 40911 HSPs Collected Number of families returned by RECON: 2660 Round Time: 00:36:59 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108453 repeats masked totaling 29272643 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033840 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90033640 bp After Masking: 57152246 bp Masked: 36.52 % -- Input Database Coverage: 130061086 bp out of 2814434834 bp ( 4.62 % ) Sampling Time: 00:18:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:14:31 (hh:mm:ss) Elapsed Time, 129468 HSPs Collected Number of families returned by RECON: 9249 Round Time: 03:38:04 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 364709 repeats masked totaling 97330334 bp(s). - TE Masking time 00:08:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004521 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 270000321 bp After Masking: 160690572 bp Masked: 40.49 % -- Input Database Coverage: 400065607 bp out of 2814434834 bp ( 14.21 % ) Sampling Time: 00:56:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 24:14:08 (hh:mm:ss) Elapsed Time, 309645 HSPs Collected Number of families returned by RECON: 36143 Round Time: 26:02:16 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatScout/RECON discovery complete: 987 families found Classification Time: 00:55:20 (hh:mm:ss) Elapsed Time Program Time: 31:58:26 (hh:mm:ss) Elapsed Time