RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.nRK6Sn/RM_19737.MonNov182244162024 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: 1731998655 Database = /scratch/tmp/rModeler.nRK6Sn/GCA_964213995.1_sMusAst1.hap1.1 - Sequences = 5314 - Bases = 3679792345 - N50 = 111213091 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188636876-202110868 | [ 1 ] 175162885-188636876 | [ ] 161688894-175162885 | [ 1 ] 148214903-161688894 | [ 3 ] 134740912-148214903 | [ 4 ] 121266920-134740911 | [ 1 ] 107792929-121266920 | [ 3 ] 94318938-107792929 | [ 3 ] 80844947-94318938 | [ 5 ] 67370956-80844947 | [ 2 ] 53896964-67370955 | [ 2 ] 40422973-53896964 | [ 2 ] 26948982-40422973 | [ 1 ] 13474991-26948982 | [ 3 ] 1000-13474991 |************************************************** [ 5283 ] Storage Throughput = fair ( 627.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007205 bp ( 40000205 non ambiguous ) - Num Contigs Represented = 221 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:57 (hh:mm:ss) Elapsed Time Round Time: 00:32:49 (hh:mm:ss) Elapsed Time : 512 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22624 repeats masked totaling 5115928 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037725 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 10036125 bp After Masking: 3885003 bp Masked: 61.29 % -- Input Database Coverage: 10037725 bp out of 3679792345 bp ( 0.27 % ) Sampling Time: 00:05:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:04:29 (hh:mm:ss) Elapsed Time, 5632 HSPs Collected Number of families returned by RECON: 925 Round Time: 00:10:11 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66384 repeats masked totaling 15408525 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009447 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 30003847 bp After Masking: 11407049 bp Masked: 61.98 % -- Input Database Coverage: 40047172 bp out of 3679792345 bp ( 1.09 % ) Sampling Time: 00:15:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:19:21 (hh:mm:ss) Elapsed Time, 43826 HSPs Collected Number of families returned by RECON: 2930 Round Time: 00:37:03 (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 : 00:04:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 216323 repeats masked totaling 49585048 bp(s). - TE Masking time 00:03:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039894 bp Num Contigs Represented = 385 Non ambiguous bp: Initial: 90020494 bp After Masking: 30933363 bp Masked: 65.64 % -- Input Database Coverage: 130087066 bp out of 3679792345 bp ( 3.54 % ) Sampling Time: 00:55:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2662278 Comparison Time: 01:49:19 (hh:mm:ss) Elapsed Time, 163840 HSPs Collected Number of families returned by RECON: 7042 Round Time: 02:54:00 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:06:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 692484 repeats masked totaling 158437234 bp(s). - TE Masking time 00:13:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053808 bp Num Contigs Represented = 1037 Non ambiguous bp: Initial: 270002285 bp After Masking: 81993209 bp Masked: 69.63 % -- Input Database Coverage: 400140874 bp out of 3679792345 bp ( 10.87 % ) Sampling Time: 02:35:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24335776 Comparison Time: 12:21:19 (hh:mm:ss) Elapsed Time, 387994 HSPs Collected Number of families returned by RECON: 19601 Round Time: 15:27:16 (hh:mm:ss) Elapsed Time : 736 families discovered. RepeatScout/RECON discovery complete: 1697 families found Classification Time: 01:20:28 (hh:mm:ss) Elapsed Time Program Time: 21:01:47 (hh:mm:ss) Elapsed Time