RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IfNHTK/RM_6666.MonDec41825122023 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: 1701743111 Database = /dev/shm/rModeler.IfNHTK/GCA_031021105.1_rEryReg1.hap1 - Sequences = 400 - Bases = 1964049041 - N50 = 355369171 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 398122580-426559836 | [ 1 ] 369685324-398122579 | [ ] 341248068-369685323 | [ 1 ] 312810813-341248068 | [ ] 284373557-312810812 | [ ] 255936301-284373556 | [ 1 ] 227499045-255936300 | [ ] 199061790-227499045 | [ ] 170624534-199061789 | [ ] 142187278-170624533 | [ 1 ] 113750022-142187277 | [ 2 ] 85312767-113750022 | [ 2 ] 56875511-85312766 | [ 2 ] 28438255-56875510 | [ 3 ] 1000-28438255 |************************************************** [ 387 ] Storage Throughput = excellent ( 1207.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013025 bp ( 40006025 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:04:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:25 (hh:mm:ss) Elapsed Time Round Time: 00:36:20 (hh:mm:ss) Elapsed Time : 686 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:15 (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... 19902 repeats masked totaling 4876744 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041381 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10039581 bp After Masking: 4709539 bp Masked: 53.09 % -- Input Database Coverage: 10041381 bp out of 1964049041 bp ( 0.51 % ) Sampling Time: 00:02:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:06 (hh:mm:ss) Elapsed Time, 5118 HSPs Collected Number of families returned by RECON: 909 Round Time: 00:08:19 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61727 repeats masked totaling 14260537 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011485 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30006285 bp After Masking: 14152371 bp Masked: 52.84 % -- Input Database Coverage: 40052866 bp out of 1964049041 bp ( 2.04 % ) Sampling Time: 00:09:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:24:40 (hh:mm:ss) Elapsed Time, 28461 HSPs Collected Number of families returned by RECON: 2983 Round Time: 00:35:02 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 194831 repeats masked totaling 44310645 bp(s). - TE Masking time 00:03:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027776 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90016781 bp After Masking: 41013275 bp Masked: 54.44 % -- Input Database Coverage: 130080642 bp out of 1964049041 bp ( 6.62 % ) Sampling Time: 00:25:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:34:17 (hh:mm:ss) Elapsed Time, 179347 HSPs Collected Number of families returned by RECON: 9077 Round Time: 03:07:26 (hh:mm:ss) Elapsed Time : 386 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:32:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 645714 repeats masked totaling 142305672 bp(s). - TE Masking time 00:14:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041599 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 270002253 bp After Masking: 113622227 bp Masked: 57.92 % -- Input Database Coverage: 400122241 bp out of 1964049041 bp ( 20.37 % ) Sampling Time: 01:22:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 18:43:02 (hh:mm:ss) Elapsed Time, 594294 HSPs Collected Number of families returned by RECON: 26672 Round Time: 20:50:32 (hh:mm:ss) Elapsed Time : 972 families discovered. RepeatScout/RECON discovery complete: 2135 families found Classification Time: 01:26:57 (hh:mm:ss) Elapsed Time Program Time: 26:44:36 (hh:mm:ss) Elapsed Time