RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VywiSJ/RM_19759.FriJan121122222024 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: 1705087341 Database = /dev/shm/rModeler.VywiSJ/GCA_031877785.1_bStrAlu1.hap2 - Sequences = 184 - Bases = 1219048950 - N50 = 132664630 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 161986720-173556185 | [ 1 ] 150417255-161986719 | [ ] 138847791-150417255 | [ ] 127278326-138847790 | [ 3 ] 115708862-127278326 | [ ] 104139397-115708861 | [ ] 92569933-104139397 | [ ] 81000468-92569932 | [ 1 ] 69431004-81000468 | [ ] 57861539-69431003 | [ ] 46292075-57861539 | [ ] 34722610-46292074 | [ 3 ] 23153146-34722610 |* [ 6 ] 11583681-23153145 |** [ 8 ] 14217-11583681 |************************************************** [ 162 ] Storage Throughput = excellent ( 1045.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40046963 bp ( 40023917 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:06 (hh:mm:ss) Elapsed Time Round Time: 00:27:35 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1351 repeats masked totaling 541720 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038064 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10038064 bp After Masking: 8940248 bp Masked: 10.94 % -- Input Database Coverage: 10038064 bp out of 1219048950 bp ( 0.82 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:08:41 (hh:mm:ss) Elapsed Time, 624 HSPs Collected Number of families returned by RECON: 243 Round Time: 00:10:57 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3737 repeats masked totaling 1539669 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30048742 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30025696 bp After Masking: 26352762 bp Masked: 12.23 % -- Input Database Coverage: 40086806 bp out of 1219048950 bp ( 3.29 % ) Sampling Time: 00:10:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 01:31:42 (hh:mm:ss) Elapsed Time, 5062 HSPs Collected Number of families returned by RECON: 1432 Round Time: 01:42:51 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:07 (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... 13189 repeats masked totaling 4861662 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90158409 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90035641 bp After Masking: 78760079 bp Masked: 12.52 % -- Input Database Coverage: 130245215 bp out of 1219048950 bp ( 10.68 % ) Sampling Time: 00:16:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 06:13:08 (hh:mm:ss) Elapsed Time, 48302 HSPs Collected Number of families returned by RECON: 8399 Round Time: 06:32:49 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50617 repeats masked totaling 17414217 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270317124 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 270032313 bp After Masking: 232441636 bp Masked: 13.92 % -- Input Database Coverage: 400562339 bp out of 1219048950 bp ( 32.86 % ) Sampling Time: 00:55:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 38:16:33 (hh:mm:ss) Elapsed Time, 250804 HSPs Collected Number of families returned by RECON: 53657 Round Time: 40:19:09 (hh:mm:ss) Elapsed Time : 269 families discovered. RepeatScout/RECON discovery complete: 394 families found Classification Time: 00:49:48 (hh:mm:ss) Elapsed Time Program Time: 50:03:09 (hh:mm:ss) Elapsed Time