RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.aarbCB/RM_1814779.MonDec21730552024 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: 1733189454 Database = /scratch/tmp/rModeler.aarbCB/GCF_036971445.1_sNarBan1.hap1 - Sequences = 595 - Bases = 3328432768 - N50 = 321486706 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 461524447-494489450 | [ 1 ] 428559445-461524447 | [ ] 395594442-428559444 | [ ] 362629440-395594442 | [ 2 ] 329664438-362629440 | [ ] 296699435-329664437 | [ 1 ] 263734433-296699435 | [ ] 230769430-263734432 | [ 2 ] 197804428-230769430 | [ 1 ] 164839426-197804428 | [ 1 ] 131874423-164839425 | [ ] 98909421-131874423 | [ 4 ] 65944418-98909420 | [ 2 ] 32979416-65944418 | [ ] 14414-32979416 |************************************************** [ 581 ] Storage Throughput = excellent ( 1093.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027239 bp ( 40022139 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:02:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:25 (hh:mm:ss) Elapsed Time Round Time: 00:17:32 (hh:mm:ss) Elapsed Time : 716 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18502 repeats masked totaling 4874379 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031121 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10030321 bp After Masking: 3655912 bp Masked: 63.55 % -- Input Database Coverage: 10031121 bp out of 3328432768 bp ( 0.30 % ) Sampling Time: 00:03:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 4294 HSPs Collected Number of families returned by RECON: 748 Round Time: 00:06:32 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56486 repeats masked totaling 14245807 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035959 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30031659 bp After Masking: 10707812 bp Masked: 64.34 % -- Input Database Coverage: 40067080 bp out of 3328432768 bp ( 1.20 % ) Sampling Time: 00:13:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:10:19 (hh:mm:ss) Elapsed Time, 32241 HSPs Collected Number of families returned by RECON: 2164 Round Time: 00:24:28 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 176492 repeats masked totaling 44642299 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018698 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90010098 bp After Masking: 30055764 bp Masked: 66.61 % -- Input Database Coverage: 130085778 bp out of 3328432768 bp ( 3.91 % ) Sampling Time: 00:39:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 00:52:56 (hh:mm:ss) Elapsed Time, 667921 HSPs Collected Number of families returned by RECON: 5565 Round Time: 01:34:52 (hh:mm:ss) Elapsed Time : 283 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:43:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 574617 repeats masked totaling 143109084 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056790 bp Num Contigs Represented = 193 Non ambiguous bp: Initial: 270036654 bp After Masking: 81361351 bp Masked: 69.87 % -- Input Database Coverage: 400142568 bp out of 3328432768 bp ( 12.02 % ) Sampling Time: 02:06:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 05:38:47 (hh:mm:ss) Elapsed Time, 4123423 HSPs Collected Number of families returned by RECON: 15392 Round Time: 07:56:53 (hh:mm:ss) Elapsed Time : 599 families discovered. RepeatScout/RECON discovery complete: 1688 families found Classification Time: 00:29:11 (hh:mm:ss) Elapsed Time Program Time: 10:49:28 (hh:mm:ss) Elapsed Time