RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HExaH4/RM_113618.FriJan131907222023 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: 1673665642 Database = /dev/shm/rModeler.HExaH4/GCA_903684855.2_fDreTuH1.2 - Sequences = 755 - Bases = 1360506095 - N50 = 55327790 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 68688393-73594634 | [ 2 ] 63782152-68688392 | [ ] 58875912-63782152 | [ 5 ] 53969671-58875911 | [ 5 ] 49063430-53969670 | [ 5 ] 44157190-49063430 | [ 4 ] 39250949-44157189 | [ 1 ] 34344708-39250948 | [ 3 ] 29438468-34344708 | [ ] 24532227-29438467 | [ ] 19625986-24532226 | [ ] 14719746-19625986 | [ ] 9813505-14719745 | [ ] 4907264-9813504 | [ 1 ] 1024-4907264 |************************************************** [ 729 ] Storage Throughput = good ( 977.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040137 bp ( 40037387 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:01 (hh:mm:ss) Elapsed Time Round Time: 00:34:50 (hh:mm:ss) Elapsed Time : 1074 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21971 repeats masked totaling 4325902 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022643 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10021543 bp After Masking: 5181011 bp Masked: 48.30 % -- Input Database Coverage: 10022643 bp out of 1360506095 bp ( 0.74 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:01 (hh:mm:ss) Elapsed Time, 11189 HSPs Collected Number of families returned by RECON: 1336 Round Time: 00:10:49 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66180 repeats masked totaling 12816158 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017414 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30015764 bp After Masking: 15412258 bp Masked: 48.65 % -- Input Database Coverage: 40040057 bp out of 1360506095 bp ( 2.94 % ) Sampling Time: 00:08:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:31:26 (hh:mm:ss) Elapsed Time, 63117 HSPs Collected Number of families returned by RECON: 4246 Round Time: 00:41:55 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 208164 repeats masked totaling 40300181 bp(s). - TE Masking time 00:04:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035693 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90029443 bp After Masking: 44823408 bp Masked: 50.21 % -- Input Database Coverage: 130075750 bp out of 1360506095 bp ( 9.56 % ) Sampling Time: 00:21:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 03:00:21 (hh:mm:ss) Elapsed Time, 297580 HSPs Collected Number of families returned by RECON: 10892 Round Time: 03:36:47 (hh:mm:ss) Elapsed Time : 633 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 702798 repeats masked totaling 137157079 bp(s). - TE Masking time 00:21:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041892 bp Num Contigs Represented = 227 Non ambiguous bp: Initial: 270024835 bp After Masking: 117910683 bp Masked: 56.33 % -- Input Database Coverage: 400117642 bp out of 1360506095 bp ( 29.41 % ) Sampling Time: 01:09:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23444128 Comparison Time: 18:23:25 (hh:mm:ss) Elapsed Time, 755717 HSPs Collected Number of families returned by RECON: 31163 Round Time: 20:14:45 (hh:mm:ss) Elapsed Time : 1259 families discovered. RepeatScout/RECON discovery complete: 3141 families found Classification Time: 02:04:01 (hh:mm:ss) Elapsed Time Program Time: 27:23:07 (hh:mm:ss) Elapsed Time