RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.36iDZn/RM_1689630.WedAug201520242025 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: 1755728423 Database = /dev/shm/rModeler.36iDZn/GCF_964194025.1_txConMacr16.3 - Sequences = 4694 - Bases = 1175981408 - N50 = 75065497 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 83311792-89262563 | [ 3 ] 77361021-83311791 | [ 2 ] 71410250-77361020 | [ 2 ] 65459479-71410249 | [ 2 ] 59508708-65459478 | [ 2 ] 53557937-59508707 | [ 1 ] 47607166-53557936 | [ 3 ] 41656396-47607166 | [ ] 35705625-41656395 | [ ] 29754854-35705624 | [ ] 23804083-29754853 | [ ] 17853312-23804082 | [ ] 11902541-17853311 | [ ] 5951770-11902540 | [ ] 1000-5951770 |************************************************** [ 4679 ] Storage Throughput = excellent ( 1606.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40052605 bp ( 40008666 non ambiguous ) - Num Contigs Represented = 192 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:39 (hh:mm:ss) Elapsed Time Round Time: 00:14:44 (hh:mm:ss) Elapsed Time : 732 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13267 repeats masked totaling 4321292 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023947 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10010747 bp After Masking: 4669422 bp Masked: 53.36 % -- Input Database Coverage: 10023947 bp out of 1175981408 bp ( 0.85 % ) Sampling Time: 00:02:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 5238 HSPs Collected Number of families returned by RECON: 693 Round Time: 00:06:12 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39966 repeats masked totaling 13713920 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043379 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 30012640 bp After Masking: 12863927 bp Masked: 57.14 % -- Input Database Coverage: 40067326 bp out of 1175981408 bp ( 3.41 % ) Sampling Time: 00:07:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 326028 Comparison Time: 00:12:01 (hh:mm:ss) Elapsed Time, 53293 HSPs Collected Number of families returned by RECON: 2442 Round Time: 00:20:31 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123358 repeats masked totaling 41381780 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90114099 bp Num Contigs Represented = 433 Non ambiguous bp: Initial: 90018463 bp After Masking: 40114406 bp Masked: 55.44 % -- Input Database Coverage: 130181425 bp out of 1175981408 bp ( 11.07 % ) Sampling Time: 00:20:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2907666 Comparison Time: 01:04:29 (hh:mm:ss) Elapsed Time, 302404 HSPs Collected Number of families returned by RECON: 7518 Round Time: 01:28:20 (hh:mm:ss) Elapsed Time : 399 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:58:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 412870 repeats masked totaling 139892864 bp(s). - TE Masking time 00:07:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270324123 bp Num Contigs Represented = 1295 Non ambiguous bp: Initial: 270020771 bp After Masking: 101090012 bp Masked: 62.56 % -- Input Database Coverage: 400505548 bp out of 1175981408 bp ( 34.06 % ) Sampling Time: 01:10:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26568405 Comparison Time: 06:05:06 (hh:mm:ss) Elapsed Time, 1417967 HSPs Collected Number of families returned by RECON: 21748 Round Time: 07:29:13 (hh:mm:ss) Elapsed Time : 924 families discovered. RepeatScout/RECON discovery complete: 2132 families found Classification Time: 01:16:08 (hh:mm:ss) Elapsed Time Program Time: 10:55:08 (hh:mm:ss) Elapsed Time