RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YvYVBV/RM_341302.MonJan91247252023 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: 1673297244 Database = /dev/shm/rModeler.YvYVBV/GCA_009819825.1_bCarCri1.pri - Sequences = 110 - Bases = 1215245693 - N50 = 31238840 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 82158913-88027262 | [ 1 ] 76290564-82158912 | [ ] 70422216-76290564 | [ ] 64553867-70422215 | [ ] 58685519-64553867 | [ ] 52817170-58685518 | [ ] 46948822-52817170 |*** [ 4 ] 41080473-46948821 |** [ 3 ] 35212125-41080473 |* [ 2 ] 29343776-35212124 |*** [ 4 ] 23475428-29343776 |**** [ 6 ] 17607079-23475427 |******** [ 11 ] 11738731-17607079 |******** [ 10 ] 5870382-11738730 |***** [ 7 ] 2034-5870382 |************************************************** [ 62 ] Storage Throughput = excellent ( 1615.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40334691 bp ( 40030740 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:37 (hh:mm:ss) Elapsed Time Round Time: 00:14:49 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1090 repeats masked totaling 513208 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001633 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10001633 bp After Masking: 9452608 bp Masked: 5.49 % -- Input Database Coverage: 10001633 bp out of 1215245693 bp ( 0.82 % ) Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:37 (hh:mm:ss) Elapsed Time, 534 HSPs Collected Number of families returned by RECON: 222 Round Time: 00:07:08 (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 : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3793 repeats masked totaling 1769295 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30332978 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30029027 bp After Masking: 28151163 bp Masked: 6.25 % -- Input Database Coverage: 40334611 bp out of 1215245693 bp ( 3.32 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:30:12 (hh:mm:ss) Elapsed Time, 6907 HSPs Collected Number of families returned by RECON: 1547 Round Time: 00:31:48 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12802 repeats masked totaling 5564048 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90381960 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90020826 bp After Masking: 84151979 bp Masked: 6.52 % -- Input Database Coverage: 130716571 bp out of 1215245693 bp ( 10.76 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:39:23 (hh:mm:ss) Elapsed Time, 38939 HSPs Collected Number of families returned by RECON: 8982 Round Time: 02:44:24 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51381 repeats masked totaling 20056675 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271187924 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270038957 bp After Masking: 248990712 bp Masked: 7.79 % -- Input Database Coverage: 401904495 bp out of 1215245693 bp ( 33.07 % ) Sampling Time: 00:11:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 19:04:27 (hh:mm:ss) Elapsed Time, 156347 HSPs Collected Number of families returned by RECON: 56477 Round Time: 19:39:15 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatScout/RECON discovery complete: 329 families found Classification Time: 00:12:49 (hh:mm:ss) Elapsed Time Program Time: 23:30:13 (hh:mm:ss) Elapsed Time