RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CYoJy7/RM_25868.SatNov252139332023 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: 1700977150 Database = /dev/shm/rModeler.CYoJy7/GCA_011750645.1_mArvNil1.mat - Sequences = 1610 - Bases = 2486141644 - N50 = 81119311 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 154513158-165549720 | [ 1 ] 143476597-154513158 | [ 1 ] 132440036-143476597 | [ 2 ] 121403474-132440035 | [ 1 ] 110366913-121403474 | [ ] 99330352-110366913 | [ 1 ] 88293790-99330351 | [ 3 ] 77257229-88293790 | [ 4 ] 66220668-77257229 | [ 3 ] 55184106-66220667 | [ 1 ] 44147545-55184106 | [ 9 ] 33110984-44147545 | [ 2 ] 22074422-33110983 | [ 2 ] 11037861-22074422 | [ 2 ] 1300-11037861 |************************************************** [ 1578 ] Storage Throughput = excellent ( 1173.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40338910 bp ( 40008954 non ambiguous ) - Num Contigs Represented = 105 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:10 (hh:mm:ss) Elapsed Time Round Time: 00:34:46 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11528 repeats masked totaling 2265461 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10056986 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10009363 bp After Masking: 7158574 bp Masked: 28.48 % -- Input Database Coverage: 10056986 bp out of 2486141644 bp ( 0.40 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:08:18 (hh:mm:ss) Elapsed Time, 171572 HSPs Collected Number of families returned by RECON: 825 Round Time: 00:10:34 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40406 repeats masked totaling 7821950 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30321844 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 30039511 bp After Masking: 20776066 bp Masked: 30.84 % -- Input Database Coverage: 40378830 bp out of 2486141644 bp ( 1.62 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:41:02 (hh:mm:ss) Elapsed Time, 510755 HSPs Collected Number of families returned by RECON: 2706 Round Time: 00:48:22 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128451 repeats masked totaling 25213227 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91059682 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 90034664 bp After Masking: 60880361 bp Masked: 32.38 % -- Input Database Coverage: 131438512 bp out of 2486141644 bp ( 5.29 % ) Sampling Time: 00:17:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2657665 Comparison Time: 04:06:51 (hh:mm:ss) Elapsed Time, 1417306 HSPs Collected Number of families returned by RECON: 9394 Round Time: 04:30:45 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 435964 repeats masked totaling 83381163 bp(s). - TE Masking time 00:07:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273248036 bp Num Contigs Represented = 405 Non ambiguous bp: Initial: 270006465 bp After Masking: 175365201 bp Masked: 35.05 % -- Input Database Coverage: 404686548 bp out of 2486141644 bp ( 16.28 % ) Sampling Time: 01:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24050580 Comparison Time: 39:55:57 (hh:mm:ss) Elapsed Time, 15424324 HSPs Collected Number of families returned by RECON: 37512 Round Time: 41:41:54 (hh:mm:ss) Elapsed Time : 403 families discovered. RepeatScout/RECON discovery complete: 995 families found Classification Time: 00:42:18 (hh:mm:ss) Elapsed Time Program Time: 48:28:39 (hh:mm:ss) Elapsed Time