RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ItJ4BD/RM_760545.TueMar260754442024 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: 1711464884 Database = /dev/shm/rModeler.ItJ4BD/GCA_963454915.1_fGymMic1.1 - Sequences = 374 - Bases = 1318656016 - N50 = 55471006 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61408029-65794246 | [ 2 ] 57021813-61408029 |* [ 7 ] 52635596-57021812 | [ 3 ] 48249380-52635596 |* [ 8 ] 43863164-48249380 | [ 2 ] 39476947-43863163 | [ ] 35090731-39476947 | [ 2 ] 30704514-35090730 | [ ] 26318298-30704514 | [ ] 21932082-26318298 | [ ] 17545865-21932081 | [ ] 13159649-17545865 | [ ] 8773432-13159648 | [ ] 4387216-8773432 | [ ] 1000-4387216 |************************************************** [ 350 ] Storage Throughput = good ( 776.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019229 bp ( 40009429 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:28 (hh:mm:ss) Elapsed Time Round Time: 00:28:02 (hh:mm:ss) Elapsed Time : 1061 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26403 repeats masked totaling 3739388 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020731 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10017731 bp After Masking: 5403978 bp Masked: 46.06 % -- Input Database Coverage: 10020731 bp out of 1318656016 bp ( 0.76 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 6361 HSPs Collected Number of families returned by RECON: 1653 Round Time: 00:08:40 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75451 repeats masked totaling 10707455 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038498 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30031698 bp After Masking: 16609031 bp Masked: 44.69 % -- Input Database Coverage: 40059229 bp out of 1318656016 bp ( 3.04 % ) Sampling Time: 00:06:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:25:16 (hh:mm:ss) Elapsed Time, 51862 HSPs Collected Number of families returned by RECON: 5949 Round Time: 00:34:26 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 239549 repeats masked totaling 33524370 bp(s). - TE Masking time 00:03:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040577 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90018816 bp After Masking: 48762313 bp Masked: 45.83 % -- Input Database Coverage: 130099806 bp out of 1318656016 bp ( 9.87 % ) Sampling Time: 00:23:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 02:30:08 (hh:mm:ss) Elapsed Time, 365908 HSPs Collected Number of families returned by RECON: 18435 Round Time: 03:10:08 (hh:mm:ss) Elapsed Time : 741 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 816678 repeats masked totaling 117294152 bp(s). - TE Masking time 00:17:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270075909 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 270015670 bp After Masking: 130368135 bp Masked: 51.72 % -- Input Database Coverage: 400175715 bp out of 1318656016 bp ( 30.35 % ) Sampling Time: 01:16:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 16:57:02 (hh:mm:ss) Elapsed Time, 1438282 HSPs Collected Number of families returned by RECON: 53275 Round Time: 19:55:35 (hh:mm:ss) Elapsed Time : 1982 families discovered. RepeatScout/RECON discovery complete: 3891 families found Classification Time: 02:24:45 (hh:mm:ss) Elapsed Time Program Time: 26:41:36 (hh:mm:ss) Elapsed Time