RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dtx8tP/RM_20932.WedMay170648452023 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: 1684331324 Database = /dev/shm/rModeler.dtx8tP/GCF_937001465.1_mOrcOrc1.1 - Sequences = 448 - Bases = 2647351467 - N50 = 120755892 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198518715-212697510 | [ 2 ] 184339920-198518714 | [ 1 ] 170161126-184339920 | [ ] 155982331-170161125 | [ ] 141803536-155982330 | [ 2 ] 127624742-141803536 | [ 1 ] 113445947-127624741 | [ 3 ] 99267152-113445946 | [ 3 ] 85088358-99267152 | [ 6 ] 70909563-85088357 | [ 1 ] 56730768-70909562 | [ 2 ] 42551974-56730768 | [ ] 28373179-42551973 | [ 1 ] 14194384-28373178 | [ ] 15590-14194384 |************************************************** [ 426 ] Storage Throughput = excellent ( 1103.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007814 bp ( 40007414 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:11 (hh:mm:ss) Elapsed Time Round Time: 00:39:13 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9358 repeats masked totaling 2638654 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039992 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10039792 bp After Masking: 7280366 bp Masked: 27.48 % -- Input Database Coverage: 10039992 bp out of 2647351467 bp ( 0.38 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:51 (hh:mm:ss) Elapsed Time, 177527 HSPs Collected Number of families returned by RECON: 859 Round Time: 00:19:48 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:55 (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... 33188 repeats masked totaling 10123953 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007663 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30007463 bp After Masking: 19440071 bp Masked: 35.22 % -- Input Database Coverage: 40047655 bp out of 2647351467 bp ( 1.51 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:30:50 (hh:mm:ss) Elapsed Time, 42177 HSPs Collected Number of families returned by RECON: 2210 Round Time: 00:35:37 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109469 repeats masked totaling 34394949 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031856 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90030656 bp After Masking: 54295854 bp Masked: 39.69 % -- Input Database Coverage: 130079511 bp out of 2647351467 bp ( 4.91 % ) Sampling Time: 00:11:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:04:35 (hh:mm:ss) Elapsed Time, 163995 HSPs Collected Number of families returned by RECON: 7840 Round Time: 03:19:48 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 363969 repeats masked totaling 109464186 bp(s). - TE Masking time 00:05:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040850 bp Num Contigs Represented = 228 Non ambiguous bp: Initial: 270038050 bp After Masking: 157029140 bp Masked: 41.85 % -- Input Database Coverage: 400120361 bp out of 2647351467 bp ( 15.11 % ) Sampling Time: 00:34:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 23:01:57 (hh:mm:ss) Elapsed Time, 1038921 HSPs Collected Number of families returned by RECON: 32632 Round Time: 24:05:37 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatScout/RECON discovery complete: 805 families found Classification Time: 00:33:25 (hh:mm:ss) Elapsed Time Program Time: 29:33:28 (hh:mm:ss) Elapsed Time