RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MA0kW8/RM_3566146.MonFeb242250072025 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: 1740466206 Database = /dev/shm/rModeler.MA0kW8/GCA_965140915.1_bAytMar2.hap1.1 - Sequences = 1269 - Bases = 1224533240 - N50 = 89030289 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193742535-207581217 | [ 1 ] 179903854-193742535 | [ ] 166065173-179903854 | [ ] 152226492-166065173 | [ 1 ] 138387811-152226492 | [ ] 124549130-138387811 | [ ] 110710449-124549130 | [ 1 ] 96871767-110710448 | [ ] 83033086-96871767 | [ 1 ] 69194405-83033086 | [ 1 ] 55355724-69194405 | [ 1 ] 41517043-55355724 | [ ] 27678362-41517043 | [ 3 ] 13839681-27678362 | [ 10 ] 1000-13839681 |************************************************** [ 1250 ] Storage Throughput = excellent ( 1714.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036866 bp ( 40032466 non ambiguous ) - Num Contigs Represented = 110 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:01 (hh:mm:ss) Elapsed Time Round Time: 00:10:48 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2452 repeats masked totaling 972619 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027771 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10027171 bp After Masking: 8591195 bp Masked: 14.32 % -- Input Database Coverage: 10027771 bp out of 1224533240 bp ( 0.82 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:37 (hh:mm:ss) Elapsed Time, 1769 HSPs Collected Number of families returned by RECON: 286 Round Time: 00:05:34 (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 : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6589 repeats masked totaling 2719823 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009037 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30005237 bp After Masking: 25928179 bp Masked: 13.59 % -- Input Database Coverage: 40036808 bp out of 1224533240 bp ( 3.27 % ) Sampling Time: 00:07:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:17:56 (hh:mm:ss) Elapsed Time, 10433 HSPs Collected Number of families returned by RECON: 1700 Round Time: 00:25:18 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22591 repeats masked totaling 9139283 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021802 bp Num Contigs Represented = 229 Non ambiguous bp: Initial: 90012602 bp After Masking: 76179581 bp Masked: 15.37 % -- Input Database Coverage: 130058610 bp out of 1224533240 bp ( 10.62 % ) Sampling Time: 00:19:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2655360 Comparison Time: 01:56:41 (hh:mm:ss) Elapsed Time, 74536 HSPs Collected Number of families returned by RECON: 9828 Round Time: 02:25:21 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73898 repeats masked totaling 28944634 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270049685 bp Num Contigs Represented = 484 Non ambiguous bp: Initial: 270018211 bp After Masking: 226971328 bp Masked: 15.94 % -- Input Database Coverage: 400108295 bp out of 1224533240 bp ( 32.67 % ) Sampling Time: 00:59:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23842965 Comparison Time: 15:37:08 (hh:mm:ss) Elapsed Time, 357063 HSPs Collected Number of families returned by RECON: 62002 Round Time: 16:58:40 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatScout/RECON discovery complete: 391 families found Classification Time: 00:16:46 (hh:mm:ss) Elapsed Time Program Time: 20:22:27 (hh:mm:ss) Elapsed Time