RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uTN0rm/RM_9039.FriJan131435002023 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: 1673649299 Database = /dev/shm/rModeler.uTN0rm/GCF_902148855.1_fSphaOr1.1 - Sequences = 340 - Bases = 1342662642 - N50 = 57338352 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 75786415-81199652 | [ 1 ] 70373179-75786415 | [ ] 64959943-70373179 | [ ] 59546707-64959943 | [ 5 ] 54133471-59546707 |* [ 11 ] 48720234-54133470 | [ 3 ] 43306998-48720234 | [ 2 ] 37893762-43306998 | [ ] 32480526-37893762 | [ ] 27067290-32480526 | [ 1 ] 21654053-27067289 | [ ] 16240817-21654053 | [ ] 10827581-16240817 | [ ] 5414345-10827581 | [ ] 1109-5414345 |************************************************** [ 317 ] Storage Throughput = excellent ( 1065.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40174219 bp ( 40034680 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:59 (hh:mm:ss) Elapsed Time Round Time: 00:30:02 (hh:mm:ss) Elapsed Time : 967 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 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16530 repeats masked totaling 3594729 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024856 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10023113 bp After Masking: 5788300 bp Masked: 42.25 % -- Input Database Coverage: 10024856 bp out of 1342662642 bp ( 0.75 % ) Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:11 (hh:mm:ss) Elapsed Time, 14418 HSPs Collected Number of families returned by RECON: 1422 Round Time: 00:09:44 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53958 repeats masked totaling 11657557 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30149360 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30011564 bp After Masking: 16373766 bp Masked: 45.44 % -- Input Database Coverage: 40174216 bp out of 1342662642 bp ( 2.99 % ) Sampling Time: 00:06:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:38:22 (hh:mm:ss) Elapsed Time, 244383 HSPs Collected Number of families returned by RECON: 4269 Round Time: 00:47:13 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168889 repeats masked totaling 35413705 bp(s). - TE Masking time 00:04:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90426994 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90018631 bp After Masking: 49039255 bp Masked: 45.52 % -- Input Database Coverage: 130601210 bp out of 1342662642 bp ( 9.73 % ) Sampling Time: 00:18:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 04:11:51 (hh:mm:ss) Elapsed Time, 2947278 HSPs Collected Number of families returned by RECON: 13033 Round Time: 04:43:15 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 581852 repeats masked totaling 120888969 bp(s). - TE Masking time 00:24:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270858643 bp Num Contigs Represented = 174 Non ambiguous bp: Initial: 270008930 bp After Masking: 131852740 bp Masked: 51.17 % -- Input Database Coverage: 401459853 bp out of 1342662642 bp ( 29.90 % ) Sampling Time: 01:06:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 25:39:23 (hh:mm:ss) Elapsed Time, 6930815 HSPs Collected Number of families returned by RECON: 39277 Round Time: 27:56:28 (hh:mm:ss) Elapsed Time : 1287 families discovered. RepeatScout/RECON discovery complete: 2996 families found Classification Time: 01:51:36 (hh:mm:ss) Elapsed Time Program Time: 35:58:18 (hh:mm:ss) Elapsed Time