RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dzX2MI/RM_17804.TueNov280516102023 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: 1701177369 Database = /dev/shm/rModeler.dzX2MI/GCA_028017845.1_rEmyOrb1.hap2 - Sequences = 156 - Bases = 2327425914 - N50 = 210333468 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 348475270-373365194 | [ 1 ] 323585346-348475269 | [ ] 298695422-323585345 | [ ] 273805499-298695422 | [ 1 ] 248915575-273805498 | [ ] 224025651-248915574 | [ 1 ] 199135727-224025650 | [ 1 ] 174245804-199135727 | [ ] 149355880-174245803 | [ ] 124465956-149355879 | [ 2 ] 99576032-124465955 | [ 2 ] 74686109-99576032 |* [ 3 ] 49796185-74686108 | [ 2 ] 24906261-49796184 |** [ 6 ] 16338-24906261 |************************************************* [ 137 ] Storage Throughput = excellent ( 1200.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019952 bp ( 40015298 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:15 (hh:mm:ss) Elapsed Time Round Time: 00:32:09 (hh:mm:ss) Elapsed Time : 638 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14642 repeats masked totaling 3144505 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040132 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10035685 bp After Masking: 6721583 bp Masked: 33.02 % -- Input Database Coverage: 10040132 bp out of 2327425914 bp ( 0.43 % ) Sampling Time: 00:02:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 14003 HSPs Collected Number of families returned by RECON: 1625 Round Time: 00:08:46 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45658 repeats masked totaling 9921757 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019824 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30019617 bp After Masking: 19766094 bp Masked: 34.16 % -- Input Database Coverage: 40059956 bp out of 2327425914 bp ( 1.72 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:28:45 (hh:mm:ss) Elapsed Time, 60495 HSPs Collected Number of families returned by RECON: 5007 Round Time: 00:36:10 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158607 repeats masked totaling 33752291 bp(s). - TE Masking time 00:02:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90321869 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90032101 bp After Masking: 55193960 bp Masked: 38.70 % -- Input Database Coverage: 130381825 bp out of 2327425914 bp ( 5.60 % ) Sampling Time: 00:16:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:57:35 (hh:mm:ss) Elapsed Time, 257811 HSPs Collected Number of families returned by RECON: 14123 Round Time: 03:26:50 (hh:mm:ss) Elapsed Time : 456 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 537231 repeats masked totaling 115764265 bp(s). - TE Masking time 00:13:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270796525 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 270006360 bp After Masking: 151337922 bp Masked: 43.95 % -- Input Database Coverage: 401178350 bp out of 2327425914 bp ( 17.24 % ) Sampling Time: 00:50:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 22:07:53 (hh:mm:ss) Elapsed Time, 1311011 HSPs Collected Number of families returned by RECON: 43862 Round Time: 24:22:53 (hh:mm:ss) Elapsed Time : 1101 families discovered. RepeatScout/RECON discovery complete: 2362 families found Classification Time: 01:44:56 (hh:mm:ss) Elapsed Time Program Time: 30:51:44 (hh:mm:ss) Elapsed Time