RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tZf4Hn/RM_26836.SatNov252138352023 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: 1700977114 Database = /dev/shm/rModeler.tZf4Hn/GCA_004115295.1_mRhiFer1_v1.h - Sequences = 13424 - Bases = 1514615512 - N50 = 301255 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 2273446-2435785 | [ 2 ] 2111108-2273446 | [ ] 1948770-2111108 | [ 1 ] 1786432-1948770 | [ 3 ] 1624094-1786432 | [ 4 ] 1461756-1624094 | [ 2 ] 1299418-1461756 | [ 16 ] 1137080-1299418 | [ 23 ] 974742-1137080 | [ 38 ] 812404-974742 | [ 74 ] 650066-812404 | [ 155 ] 487728-650066 |* [ 321 ] 325390-487728 |** [ 620 ] 163052-325390 |****** [ 1417 ] 714-163052 |************************************************** [ 10748 ] Storage Throughput = excellent ( 1233.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040766 bp ( 40040766 non ambiguous ) - Num Contigs Represented = 1057 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:49 (hh:mm:ss) Elapsed Time Round Time: 00:26:54 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7151 repeats masked totaling 1832771 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012506 bp Num Contigs Represented = 287 Non ambiguous bp: Initial: 10012506 bp After Masking: 8105150 bp Masked: 19.05 % -- Input Database Coverage: 10012506 bp out of 1514615512 bp ( 0.66 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42778 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 7240 HSPs Collected Number of families returned by RECON: 994 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26128 repeats masked totaling 6300005 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028188 bp Num Contigs Represented = 806 Non ambiguous bp: Initial: 30028188 bp After Masking: 23492574 bp Masked: 21.76 % -- Input Database Coverage: 40040694 bp out of 1514615512 bp ( 2.64 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 383250 Comparison Time: 00:33:34 (hh:mm:ss) Elapsed Time, 31318 HSPs Collected Number of families returned by RECON: 2760 Round Time: 00:36:39 (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 : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90148 repeats masked totaling 22126241 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019139 bp Num Contigs Represented = 2111 Non ambiguous bp: Initial: 90019139 bp After Masking: 67147452 bp Masked: 25.41 % -- Input Database Coverage: 130059833 bp out of 1514615512 bp ( 8.59 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3407355 Comparison Time: 03:42:10 (hh:mm:ss) Elapsed Time, 73730 HSPs Collected Number of families returned by RECON: 9545 Round Time: 03:50:44 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 306249 repeats masked totaling 73817983 bp(s). - TE Masking time 00:05:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270006730 bp Num Contigs Represented = 4792 Non ambiguous bp: Initial: 270006230 bp After Masking: 193967178 bp Masked: 28.16 % -- Input Database Coverage: 400066563 bp out of 1514615512 bp ( 26.41 % ) Sampling Time: 00:13:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 30533205 Comparison Time: 28:39:53 (hh:mm:ss) Elapsed Time, 240253 HSPs Collected Number of families returned by RECON: 41950 Round Time: 29:34:56 (hh:mm:ss) Elapsed Time : 381 families discovered. RepeatScout/RECON discovery complete: 791 families found Classification Time: 00:38:06 (hh:mm:ss) Elapsed Time Program Time: 35:15:03 (hh:mm:ss) Elapsed Time