RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.UEdZLq/RM_1110828.ThuNov142334412024 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: 1731656080 Database = /scratch/tmp/rModeler.UEdZLq/GCF_028017835.1_rEmyOrb1.hap1 - Sequences = 106 - Bases = 2309740635 - N50 = 158421364 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 348960482-373885020 | [ 1 ] 324035945-348960482 | [ ] 299111408-324035945 | [ 1 ] 274186871-299111408 | [ ] 249262334-274186871 | [ ] 224337796-249262333 | [ ] 199413259-224337796 | [ 1 ] 174488722-199413259 | [ ] 149564185-174488722 | [ 1 ] 124639648-149564185 |* [ 3 ] 99715110-124639647 |* [ 2 ] 74790573-99715110 |* [ 2 ] 49866036-74790573 |* [ 2 ] 24941499-49866036 |*** [ 6 ] 16962-24941499 |************************************************** [ 87 ] Storage Throughput = excellent ( 1450.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40059757 bp ( 40019036 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:30 (hh:mm:ss) Elapsed Time Round Time: 00:11:48 (hh:mm:ss) Elapsed Time : 601 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13834 repeats masked totaling 3073264 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030281 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10030081 bp After Masking: 6841978 bp Masked: 31.79 % -- Input Database Coverage: 10030281 bp out of 2309740635 bp ( 0.43 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 13143 HSPs Collected Number of families returned by RECON: 1697 Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45003 repeats masked totaling 9622736 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30069325 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30028804 bp After Masking: 20030950 bp Masked: 33.29 % -- Input Database Coverage: 40099606 bp out of 2309740635 bp ( 1.74 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:33 (hh:mm:ss) Elapsed Time, 84786 HSPs Collected Number of families returned by RECON: 5225 Round Time: 00:17:57 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154175 repeats masked totaling 33027367 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90092054 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90020258 bp After Masking: 56007613 bp Masked: 37.78 % -- Input Database Coverage: 130191660 bp out of 2309740635 bp ( 5.64 % ) Sampling Time: 00:07:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:17:04 (hh:mm:ss) Elapsed Time, 298192 HSPs Collected Number of families returned by RECON: 13810 Round Time: 01:30:58 (hh:mm:ss) Elapsed Time : 441 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 533070 repeats masked totaling 115934709 bp(s). - TE Masking time 00:04:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270371864 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 270021087 bp After Masking: 151190403 bp Masked: 44.01 % -- Input Database Coverage: 400563524 bp out of 2309740635 bp ( 17.34 % ) Sampling Time: 00:23:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 07:51:58 (hh:mm:ss) Elapsed Time, 1174642 HSPs Collected Number of families returned by RECON: 45521 Round Time: 08:47:07 (hh:mm:ss) Elapsed Time : 1125 families discovered. RepeatScout/RECON discovery complete: 2348 families found Classification Time: 00:48:50 (hh:mm:ss) Elapsed Time Program Time: 11:40:36 (hh:mm:ss) Elapsed Time