RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mSWdh3/RM_635285.MonOct282120092024 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: 1730175609 Database = /dev/shm/rModeler.mSWdh3/GCF_040807025.1_bStrCam1.hap1 - Sequences = 262 - Bases = 1452018929 - N50 = 89934196 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 210537049-225574516 | [ 1 ] 195499583-210537049 | [ ] 180462116-195499582 | [ ] 165424650-180462116 | [ 1 ] 150387184-165424650 | [ ] 135349717-150387183 | [ 1 ] 120312251-135349717 | [ ] 105274784-120312250 | [ ] 90237318-105274784 | [ ] 75199852-90237318 | [ 3 ] 60162385-75199851 | [ 1 ] 45124919-60162385 | [ 1 ] 30087452-45124918 | [ 4 ] 15049986-30087452 |** [ 10 ] 12520-15049986 |************************************************** [ 240 ] Storage Throughput = excellent ( 1900.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031907 bp ( 40031707 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:03 (hh:mm:ss) Elapsed Time Round Time: 00:23:40 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1127 repeats masked totaling 728477 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010633 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10010633 bp After Masking: 8519432 bp Masked: 14.90 % -- Input Database Coverage: 10010633 bp out of 1452018929 bp ( 0.69 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:03 (hh:mm:ss) Elapsed Time, 949 HSPs Collected Number of families returned by RECON: 259 Round Time: 00:04:32 (hh:mm:ss) Elapsed Time : 4 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 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3149 repeats masked totaling 1932826 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021194 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30020994 bp After Masking: 26135432 bp Masked: 12.94 % -- Input Database Coverage: 40031827 bp out of 1452018929 bp ( 2.76 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:14:46 (hh:mm:ss) Elapsed Time, 9693 HSPs Collected Number of families returned by RECON: 1516 Round Time: 00:18:19 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11661 repeats masked totaling 5390596 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010658 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90009258 bp After Masking: 79080436 bp Masked: 12.14 % -- Input Database Coverage: 130042485 bp out of 1452018929 bp ( 8.96 % ) Sampling Time: 00:08:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:35:15 (hh:mm:ss) Elapsed Time, 90464 HSPs Collected Number of families returned by RECON: 8149 Round Time: 01:51:57 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49628 repeats masked totaling 22051296 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034626 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 270028286 bp After Masking: 231000742 bp Masked: 14.45 % -- Input Database Coverage: 400077111 bp out of 1452018929 bp ( 27.55 % ) Sampling Time: 00:26:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 10:57:58 (hh:mm:ss) Elapsed Time, 562210 HSPs Collected Number of families returned by RECON: 48239 Round Time: 11:48:22 (hh:mm:ss) Elapsed Time : 285 families discovered. RepeatScout/RECON discovery complete: 431 families found Classification Time: 00:34:49 (hh:mm:ss) Elapsed Time Program Time: 15:01:39 (hh:mm:ss) Elapsed Time