RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zRlxrP/RM_3980953.MonMar180252412024 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: 1710755561 Database = /dev/shm/rModeler.zRlxrP/GCA_036172605.1_aPelFus1.pri - Sequences = 160 - Bases = 3606474367 - N50 = 427915699 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 466172540-499470508 | [ 1 ] 432874573-466172540 | [ 1 ] 399576606-432874573 | [ 1 ] 366278639-399576606 | [ 2 ] 332980672-366278639 | [ ] 299682704-332980671 | [ 1 ] 266384737-299682704 | [ ] 233086770-266384737 | [ ] 199788803-233086770 | [ 1 ] 166490836-199788803 | [ 2 ] 133192868-166490835 |* [ 3 ] 99894901-133192868 | [ 1 ] 66596934-99894901 | [ ] 33298967-66596934 | [ ] 1000-33298967 |************************************************** [ 147 ] Storage Throughput = excellent ( 1062.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003287 bp ( 40002887 non ambiguous ) - Num Contigs Represented = 17 - Sequence extraction : 00:06:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:22 (hh:mm:ss) Elapsed Time Round Time: 00:37:48 (hh:mm:ss) Elapsed Time : 781 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14676 repeats masked totaling 4508779 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001860 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 10001860 bp After Masking: 4650166 bp Masked: 53.51 % -- Input Database Coverage: 10001860 bp out of 3606474367 bp ( 0.28 % ) Sampling Time: 00:03:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 20617 HSPs Collected Number of families returned by RECON: 1230 Round Time: 00:09:02 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47129 repeats masked totaling 13742868 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001426 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 30001026 bp After Masking: 13246805 bp Masked: 55.85 % -- Input Database Coverage: 40003286 bp out of 3606474367 bp ( 1.11 % ) Sampling Time: 00:12:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:21 (hh:mm:ss) Elapsed Time, 53065 HSPs Collected Number of families returned by RECON: 4126 Round Time: 00:37:45 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:16:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151819 repeats masked totaling 43147067 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020246 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90018420 bp After Masking: 38499972 bp Masked: 57.23 % -- Input Database Coverage: 130023532 bp out of 3606474367 bp ( 3.61 % ) Sampling Time: 00:39:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:07:16 (hh:mm:ss) Elapsed Time, 294293 HSPs Collected Number of families returned by RECON: 12437 Round Time: 02:55:59 (hh:mm:ss) Elapsed Time : 429 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:46:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:05:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 503994 repeats masked totaling 139538084 bp(s). - TE Masking time 00:11:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044077 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 270039277 bp After Masking: 103401196 bp Masked: 61.71 % -- Input Database Coverage: 400067609 bp out of 3606474367 bp ( 11.09 % ) Sampling Time: 02:03:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 14:25:41 (hh:mm:ss) Elapsed Time, 840006 HSPs Collected Number of families returned by RECON: 32100 Round Time: 17:10:17 (hh:mm:ss) Elapsed Time : 1180 families discovered. RepeatScout/RECON discovery complete: 2506 families found Classification Time: 01:37:38 (hh:mm:ss) Elapsed Time Program Time: 23:08:29 (hh:mm:ss) Elapsed Time