RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gIXTfq/RM_31026.ThuJan120106102023 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: 1673514369 Database = /dev/shm/rModeler.gIXTfq/GCF_009829155.1_mMusErm1.Pri - Sequences = 94 - Bases = 2445217270 Storage Throughput = excellent ( 1092.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40219480 bp ( 40004523 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:41 (hh:mm:ss) Elapsed Time Round Time: 00:31:49 (hh:mm:ss) Elapsed Time : 148 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9435 repeats masked totaling 2280439 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080374 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10025422 bp After Masking: 7702225 bp Masked: 23.17 % -- Input Database Coverage: 10080374 bp out of 2445217270 bp ( 0.41 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 8936 HSPs Collected Number of families returned by RECON: 974 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33537 repeats masked totaling 7917221 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30179101 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30019096 bp After Masking: 21934660 bp Masked: 26.93 % -- Input Database Coverage: 40259475 bp out of 2445217270 bp ( 1.65 % ) Sampling Time: 00:03:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:34:28 (hh:mm:ss) Elapsed Time, 20196 HSPs Collected Number of families returned by RECON: 2341 Round Time: 00:38:45 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108555 repeats masked totaling 25395666 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90887242 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90027106 bp After Masking: 64139690 bp Masked: 28.76 % -- Input Database Coverage: 131146717 bp out of 2445217270 bp ( 5.36 % ) Sampling Time: 00:10:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:48:22 (hh:mm:ss) Elapsed Time, 73572 HSPs Collected Number of families returned by RECON: 8615 Round Time: 04:03:19 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 375078 repeats masked totaling 85198149 bp(s). - TE Masking time 00:05:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272709854 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 270023317 bp After Masking: 183517650 bp Masked: 32.04 % -- Input Database Coverage: 403856571 bp out of 2445217270 bp ( 16.52 % ) Sampling Time: 00:32:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 28:52:27 (hh:mm:ss) Elapsed Time, 239512 HSPs Collected Number of families returned by RECON: 36989 Round Time: 29:56:07 (hh:mm:ss) Elapsed Time : 295 families discovered. RepeatScout/RECON discovery complete: 684 families found Classification Time: 00:28:21 (hh:mm:ss) Elapsed Time Program Time: 35:46:48 (hh:mm:ss) Elapsed Time