RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yTxHkX/RM_4940.SatDec20020102023 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: 1701505209 Database = /dev/shm/rModeler.yTxHkX/GCA_030035585.1_mDugDug1.hap1 - Sequences = 198 - Bases = 3158488110 - N50 = 177379183 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215529461-230923939 | [ 1 ] 200134983-215529460 | [ 1 ] 184740505-200134982 |* [ 4 ] 169346027-184740504 | [ 1 ] 153951550-169346027 | [ ] 138557072-153951549 | [ 2 ] 123162594-138557071 | [ 3 ] 107768116-123162593 | [ 3 ] 92373638-107768115 | [ 1 ] 76979161-92373638 |* [ 5 ] 61584683-76979160 | [ 3 ] 46190205-61584682 | [ ] 30795727-46190204 | [ ] 15401249-30795726 | [ ] 6772-15401249 |************************************************** [ 174 ] Storage Throughput = excellent ( 1169.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028482 bp ( 40028082 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:55 (hh:mm:ss) Elapsed Time Round Time: 00:33:33 (hh:mm:ss) Elapsed Time : 245 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12202 repeats masked totaling 4424646 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003605 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10003605 bp After Masking: 5534403 bp Masked: 44.68 % -- Input Database Coverage: 10003605 bp out of 3158488110 bp ( 0.32 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 5823 HSPs Collected Number of families returned by RECON: 726 Round Time: 00:06:49 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40941 repeats masked totaling 13688980 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024797 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30024397 bp After Masking: 16178697 bp Masked: 46.11 % -- Input Database Coverage: 40028402 bp out of 3158488110 bp ( 1.27 % ) Sampling Time: 00:04:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:26:16 (hh:mm:ss) Elapsed Time, 24573 HSPs Collected Number of families returned by RECON: 2279 Round Time: 00:31:29 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133181 repeats masked totaling 43525329 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017669 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90016669 bp After Masking: 46015252 bp Masked: 48.88 % -- Input Database Coverage: 130046071 bp out of 3158488110 bp ( 4.12 % ) Sampling Time: 00:12:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:43:59 (hh:mm:ss) Elapsed Time, 168063 HSPs Collected Number of families returned by RECON: 7041 Round Time: 02:59:42 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438918 repeats masked totaling 136422961 bp(s). - TE Masking time 00:07:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023369 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270022169 bp After Masking: 132289433 bp Masked: 51.01 % -- Input Database Coverage: 400069440 bp out of 3158488110 bp ( 12.67 % ) Sampling Time: 00:38:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 20:37:12 (hh:mm:ss) Elapsed Time, 663852 HSPs Collected Number of families returned by RECON: 27404 Round Time: 21:41:43 (hh:mm:ss) Elapsed Time : 323 families discovered. RepeatScout/RECON discovery complete: 816 families found Classification Time: 00:34:38 (hh:mm:ss) Elapsed Time Program Time: 26:27:54 (hh:mm:ss) Elapsed Time