RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.95sNrO/RM_3950262.WedJun260404242024 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: 1719399864 Database = /dev/shm/rModeler.95sNrO/GCF_036370855.1_bDroNov1.hap1 - Sequences = 271 - Bases = 1468706110 - N50 = 85985397 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204894883-219529801 | [ 1 ] 190259965-204894882 | [ ] 175625047-190259964 | [ ] 160990129-175625046 | [ 1 ] 146355211-160990128 | [ ] 131720293-146355210 | [ 1 ] 117085375-131720292 | [ ] 102450457-117085374 | [ ] 87815539-102450456 | [ 1 ] 73180621-87815538 | [ 2 ] 58545703-73180620 | [ 1 ] 43910785-58545702 | [ 2 ] 29275867-43910784 | [ 3 ] 14640949-29275866 |** [ 10 ] 6032-14640949 |************************************************* [ 249 ] Storage Throughput = excellent ( 1177.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022485 bp ( 40021685 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:44 (hh:mm:ss) Elapsed Time Round Time: 00:38:43 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 749 repeats masked totaling 373707 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005661 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10005461 bp After Masking: 9186233 bp Masked: 8.19 % -- Input Database Coverage: 10005661 bp out of 1468706110 bp ( 0.68 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:55 (hh:mm:ss) Elapsed Time, 1832 HSPs Collected Number of families returned by RECON: 365 Round Time: 00:09:08 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3853 repeats masked totaling 1867357 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016823 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30016223 bp After Masking: 26916287 bp Masked: 10.33 % -- Input Database Coverage: 40022484 bp out of 1468706110 bp ( 2.73 % ) Sampling Time: 00:04:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:34:32 (hh:mm:ss) Elapsed Time, 13298 HSPs Collected Number of families returned by RECON: 1742 Round Time: 00:41:11 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15085 repeats masked totaling 6068801 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016969 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90016369 bp After Masking: 78600232 bp Masked: 12.68 % -- Input Database Coverage: 130039453 bp out of 1468706110 bp ( 8.85 % ) Sampling Time: 00:14:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:50:55 (hh:mm:ss) Elapsed Time, 66569 HSPs Collected Number of families returned by RECON: 8788 Round Time: 04:23:00 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61076 repeats masked totaling 24435303 bp(s). - TE Masking time 00:06:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023904 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 270019704 bp After Masking: 228859435 bp Masked: 15.24 % -- Input Database Coverage: 400063357 bp out of 1468706110 bp ( 27.24 % ) Sampling Time: 00:50:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 28:02:08 (hh:mm:ss) Elapsed Time, 338216 HSPs Collected Number of families returned by RECON: 50015 Round Time: 29:52:19 (hh:mm:ss) Elapsed Time : 325 families discovered. RepeatScout/RECON discovery complete: 522 families found Classification Time: 01:37:52 (hh:mm:ss) Elapsed Time Program Time: 37:22:13 (hh:mm:ss) Elapsed Time