RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Wf2CcF/RM_3200082.SunMay40829042025 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: 1746372541 Database = /data/tmp/rModeler.Wf2CcF/GCA_037953035.1_aLitCat1_p1.0 - Sequences = 4071 - Bases = 6623830220 - N50 = 4277981 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32043264-34330989 | [ 1 ] 29755540-32043264 | [ ] 27467815-29755539 | [ 1 ] 25180091-27467815 | [ ] 22892367-25180091 | [ ] 20604642-22892366 | [ 1 ] 18316918-20604642 | [ 6 ] 16029193-18316917 | [ 5 ] 13741469-16029193 | [ 17 ] 11453745-13741469 | [ 23 ] 9166020-11453744 | [ 35 ] 6878296-9166020 |* [ 98 ] 4590571-6878295 |*** [ 204 ] 2302847-4590571 |******** [ 521 ] 15123-2302847 |************************************************** [ 3159 ] Storage Throughput = excellent ( 1087.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015510 bp ( 40015510 non ambiguous ) - Num Contigs Represented = 748 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:21 (hh:mm:ss) Elapsed Time Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 1048 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19277 repeats masked totaling 5186477 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010746 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 10010746 bp After Masking: 4091502 bp Masked: 59.13 % -- Input Database Coverage: 10010746 bp out of 6623830220 bp ( 0.15 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 13318 HSPs Collected Number of families returned by RECON: 1618 Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56974 repeats masked totaling 15720389 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004684 bp Num Contigs Represented = 601 Non ambiguous bp: Initial: 30004684 bp After Masking: 12056374 bp Masked: 59.82 % -- Input Database Coverage: 40015430 bp out of 6623830220 bp ( 0.60 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:20:20 (hh:mm:ss) Elapsed Time, 68498 HSPs Collected Number of families returned by RECON: 4947 Round Time: 00:31:55 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 180032 repeats masked totaling 49361306 bp(s). - TE Masking time 00:02:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023235 bp Num Contigs Represented = 1274 Non ambiguous bp: Initial: 90023235 bp After Masking: 33832112 bp Masked: 62.42 % -- Input Database Coverage: 130038665 bp out of 6623830220 bp ( 1.96 % ) Sampling Time: 00:14:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 01:47:04 (hh:mm:ss) Elapsed Time, 372195 HSPs Collected Number of families returned by RECON: 13593 Round Time: 02:39:56 (hh:mm:ss) Elapsed Time : 616 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 610383 repeats masked totaling 169817433 bp(s). - TE Masking time 00:12:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016504 bp Num Contigs Represented = 2073 Non ambiguous bp: Initial: 270016504 bp After Masking: 79565346 bp Masked: 70.53 % -- Input Database Coverage: 400055169 bp out of 6623830220 bp ( 6.04 % ) Sampling Time: 00:45:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 10:51:36 (hh:mm:ss) Elapsed Time, 1006465 HSPs Collected Number of families returned by RECON: 31745 Round Time: 13:49:17 (hh:mm:ss) Elapsed Time : 1584 families discovered. RepeatScout/RECON discovery complete: 3395 families found Classification Time: 01:54:08 (hh:mm:ss) Elapsed Time Program Time: 19:31:57 (hh:mm:ss) Elapsed Time