RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NV4vmq/RM_8322.TueJul91948572024 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: 1720579736 Database = /dev/shm/rModeler.NV4vmq/GCF_001858045.2_O_niloticus_UMD_NMBU - Sequences = 2460 - Bases = 1005681550 - N50 = 39199643 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 81729881-87567345 | [ 1 ] 75892418-81729881 | [ ] 70054954-75892417 | [ ] 64217491-70054954 | [ 1 ] 58380027-64217490 | [ ] 52542564-58380027 | [ ] 46705100-52542563 | [ ] 40867637-46705100 | [ 2 ] 35030173-40867636 | [ 14 ] 29192710-35030173 | [ 4 ] 23355246-29192709 | [ ] 17517783-23355246 | [ ] 11680319-17517782 | [ ] 5842856-11680319 | [ ] 5393-5842856 |************************************************** [ 2438 ] Storage Throughput = excellent ( 1095.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005170 bp ( 40003870 non ambiguous ) - Num Contigs Represented = 150 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:38 (hh:mm:ss) Elapsed Time Round Time: 00:40:34 (hh:mm:ss) Elapsed Time : 744 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11451 repeats masked totaling 2672218 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008958 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10008358 bp After Masking: 7195373 bp Masked: 28.11 % -- Input Database Coverage: 10008958 bp out of 1005681550 bp ( 1.00 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 6184 HSPs Collected Number of families returned by RECON: 1308 Round Time: 00:06:37 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33102 repeats masked totaling 7842276 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036064 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 30035364 bp After Masking: 21697340 bp Masked: 27.76 % -- Input Database Coverage: 40045022 bp out of 1005681550 bp ( 3.98 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 309291 Comparison Time: 00:30:15 (hh:mm:ss) Elapsed Time, 41379 HSPs Collected Number of families returned by RECON: 4573 Round Time: 00:34:51 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111356 repeats masked totaling 25983741 bp(s). - TE Masking time 00:03:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044502 bp Num Contigs Represented = 327 Non ambiguous bp: Initial: 90038902 bp After Masking: 62350860 bp Masked: 30.75 % -- Input Database Coverage: 130089524 bp out of 1005681550 bp ( 12.94 % ) Sampling Time: 00:09:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2807265 Comparison Time: 03:32:20 (hh:mm:ss) Elapsed Time, 258948 HSPs Collected Number of families returned by RECON: 14609 Round Time: 03:56:41 (hh:mm:ss) Elapsed Time : 458 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 390339 repeats masked totaling 92723520 bp(s). - TE Masking time 00:16:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040700 bp Num Contigs Represented = 807 Non ambiguous bp: Initial: 270026544 bp After Masking: 172608890 bp Masked: 36.08 % -- Input Database Coverage: 400130224 bp out of 1005681550 bp ( 39.79 % ) Sampling Time: 00:34:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25173060 Comparison Time: 26:33:26 (hh:mm:ss) Elapsed Time, 797180 HSPs Collected Number of families returned by RECON: 51738 Round Time: 29:12:44 (hh:mm:ss) Elapsed Time : 1190 families discovered. RepeatScout/RECON discovery complete: 2507 families found Classification Time: 02:36:42 (hh:mm:ss) Elapsed Time Program Time: 37:08:09 (hh:mm:ss) Elapsed Time