RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.OBPrx0/RM_1662.TueNov120807562024 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: 1731427675 Database = /dev/shm/rModeler.OBPrx0/GCA_964194185.1_mRhiHip2.hap1.1 - Sequences = 723 - Bases = 2171328640 - N50 = 93091723 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 119207703-127722468 | [ 1 ] 110692938-119207702 | [ 2 ] 102178174-110692938 | [ 3 ] 93663409-102178173 | [ 3 ] 85148645-93663409 | [ 2 ] 76633880-85148644 | [ 2 ] 68119116-76633880 | [ 3 ] 59604351-68119115 | [ 2 ] 51089587-59604351 | [ 3 ] 42574822-51089586 | [ 3 ] 34060058-42574822 | [ 1 ] 25545293-34060057 | [ 2 ] 17030529-25545293 | [ 1 ] 8515764-17030528 | [ 1 ] 1000-8515764 |************************************************** [ 694 ] Storage Throughput = excellent ( 1198.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012465 bp ( 40007665 non ambiguous ) - Num Contigs Represented = 66 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:03 (hh:mm:ss) Elapsed Time Round Time: 00:33:29 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7078 repeats masked totaling 2132093 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022354 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10021554 bp After Masking: 7635487 bp Masked: 23.81 % -- Input Database Coverage: 10022354 bp out of 2171328640 bp ( 0.46 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:33 (hh:mm:ss) Elapsed Time, 40078 HSPs Collected Number of families returned by RECON: 849 Round Time: 00:10:08 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25163 repeats masked totaling 7716240 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030031 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30025831 bp After Masking: 21725021 bp Masked: 27.65 % -- Input Database Coverage: 40052385 bp out of 2171328640 bp ( 1.84 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:27:55 (hh:mm:ss) Elapsed Time, 29210 HSPs Collected Number of families returned by RECON: 2663 Round Time: 00:38:49 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90719 repeats masked totaling 25620548 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017034 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 90006525 bp After Masking: 62691761 bp Masked: 30.35 % -- Input Database Coverage: 130069419 bp out of 2171328640 bp ( 5.99 % ) Sampling Time: 00:13:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:19:39 (hh:mm:ss) Elapsed Time, 75304 HSPs Collected Number of families returned by RECON: 8070 Round Time: 03:36:29 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 300277 repeats masked totaling 83645278 bp(s). - TE Masking time 00:06:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053199 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 270018107 bp After Masking: 180985984 bp Masked: 32.97 % -- Input Database Coverage: 400122618 bp out of 2171328640 bp ( 18.43 % ) Sampling Time: 00:42:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 26:16:01 (hh:mm:ss) Elapsed Time, 191599 HSPs Collected Number of families returned by RECON: 35945 Round Time: 27:35:32 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatScout/RECON discovery complete: 805 families found Classification Time: 00:40:44 (hh:mm:ss) Elapsed Time Program Time: 33:15:11 (hh:mm:ss) Elapsed Time