RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SEnmFj/RM_168868.ThuJul41025052024 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: 1720113902 Database = /dev/shm/rModeler.SEnmFj/GCF_036934945.1_UVic_Omas_1.1 - Sequences = 17263 - Bases = 2664802492 - N50 = 71977798 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 110924508-118847666 | [ 1 ] 103001350-110924508 | [ 1 ] 95078192-103001350 | [ 4 ] 87155034-95078192 | [ 3 ] 79231876-87155034 | [ 3 ] 71308718-79231876 | [ 2 ] 63385560-71308718 | [ 2 ] 55462402-63385560 | [ 3 ] 47539244-55462402 | [ 5 ] 39616086-47539244 | [ 4 ] 31692928-39616086 | [ 2 ] 23769770-31692928 | [ 2 ] 15846612-23769770 | [ 1 ] 7923454-15846612 | [ ] 296-7923454 |************************************************** [ 17230 ] Storage Throughput = excellent ( 1310.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027555 bp ( 40003055 non ambiguous ) - Num Contigs Represented = 371 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:03 (hh:mm:ss) Elapsed Time Round Time: 00:20:11 (hh:mm:ss) Elapsed Time : 767 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13328 repeats masked totaling 3554670 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027938 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 10021538 bp After Masking: 4020308 bp Masked: 59.88 % -- Input Database Coverage: 10027938 bp out of 2664802492 bp ( 0.38 % ) Sampling Time: 00:05:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 41328 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 11169 HSPs Collected Number of families returned by RECON: 1116 Round Time: 00:11:00 (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 : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40043 repeats masked totaling 10668052 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039674 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 30021574 bp After Masking: 11571699 bp Masked: 61.46 % -- Input Database Coverage: 40067612 bp out of 2664802492 bp ( 1.50 % ) Sampling Time: 00:18:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 385003 Comparison Time: 00:17:08 (hh:mm:ss) Elapsed Time, 36563 HSPs Collected Number of families returned by RECON: 3292 Round Time: 00:37:09 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:57:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125946 repeats masked totaling 32910117 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90056165 bp Num Contigs Represented = 846 Non ambiguous bp: Initial: 90002533 bp After Masking: 33555072 bp Masked: 62.72 % -- Input Database Coverage: 130123777 bp out of 2664802492 bp ( 4.88 % ) Sampling Time: 01:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3571128 Comparison Time: 01:23:35 (hh:mm:ss) Elapsed Time, 212902 HSPs Collected Number of families returned by RECON: 9954 Round Time: 02:31:44 (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 : 00:08:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:41:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420530 repeats masked totaling 107718988 bp(s). - TE Masking time 00:04:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270161754 bp Num Contigs Represented = 2340 Non ambiguous bp: Initial: 270001630 bp After Masking: 90047450 bp Masked: 66.65 % -- Input Database Coverage: 400285531 bp out of 2664802492 bp ( 15.02 % ) Sampling Time: 02:54:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32068036 Comparison Time: 08:07:03 (hh:mm:ss) Elapsed Time, 506884 HSPs Collected Number of families returned by RECON: 32834 Round Time: 11:24:13 (hh:mm:ss) Elapsed Time : 879 families discovered. RepeatScout/RECON discovery complete: 2212 families found Classification Time: 00:58:32 (hh:mm:ss) Elapsed Time Program Time: 16:02:49 (hh:mm:ss) Elapsed Time