RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uLooz7/RM_1006087.ThuFeb61843562025 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: 1738896236 Database = /dev/shm/rModeler.uLooz7/GCF_043641665.1_fEnoArm2.hap1 - Sequences = 136 - Bases = 579897767 - N50 = 25727811 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29288228-31379816 | [ 1 ] 27196640-29288227 |** [ 6 ] 25105052-27196639 |* [ 4 ] 23013465-25105052 |* [ 4 ] 20921877-23013464 |* [ 4 ] 18830289-20921876 | [ 2 ] 16738701-18830288 | [ 1 ] 14647114-16738701 | [ 1 ] 12555526-14647113 | [ 1 ] 10463938-12555525 | [ ] 8372350-10463937 | [ ] 6280763-8372350 | [ ] 4189175-6280762 | [ ] 2097587-4189174 | [ ] 6000-2097587 |************************************************* [ 112 ] Storage Throughput = excellent ( 1443.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020023 bp ( 40017423 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:53 (hh:mm:ss) Elapsed Time Round Time: 00:09:27 (hh:mm:ss) Elapsed Time : 241 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6607 repeats masked totaling 798108 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018454 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10017254 bp After Masking: 9053293 bp Masked: 9.62 % -- Input Database Coverage: 10018454 bp out of 579897767 bp ( 1.73 % ) Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 6512 HSPs Collected Number of families returned by RECON: 1502 Round Time: 00:03:16 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20407 repeats masked totaling 2323737 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001489 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30000089 bp After Masking: 27026306 bp Masked: 9.91 % -- Input Database Coverage: 40019943 bp out of 579897767 bp ( 6.90 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:13:38 (hh:mm:ss) Elapsed Time, 53097 HSPs Collected Number of families returned by RECON: 6263 Round Time: 00:15:31 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73419 repeats masked totaling 8950368 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005493 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90001493 bp After Masking: 79225111 bp Masked: 11.97 % -- Input Database Coverage: 130025436 bp out of 579897767 bp ( 22.42 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:28:25 (hh:mm:ss) Elapsed Time, 280184 HSPs Collected Number of families returned by RECON: 23182 Round Time: 01:37:04 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 285683 repeats masked totaling 35974640 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038679 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270029279 bp After Masking: 228443114 bp Masked: 15.40 % -- Input Database Coverage: 400064115 bp out of 579897767 bp ( 68.99 % ) Sampling Time: 00:10:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 10:44:03 (hh:mm:ss) Elapsed Time, 993205 HSPs Collected Number of families returned by RECON: 93843 Round Time: 11:56:33 (hh:mm:ss) Elapsed Time : 1054 families discovered. RepeatScout/RECON discovery complete: 1806 families found Classification Time: 00:29:22 (hh:mm:ss) Elapsed Time Program Time: 14:31:13 (hh:mm:ss) Elapsed Time