RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sAuH12/RM_2411351.SatJan131644412024 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: 1705193080 Database = /dev/shm/rModeler.sAuH12/GCF_028878055.1_NHGRI_mSymSyn1-v1.1-hic.freeze_pri - Sequences = 605 - Bases = 3182923232 - N50 = 145484349 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 157506043-168756149 | [ 6 ] 146255938-157506043 | [ 3 ] 135005833-146255938 | [ 3 ] 123755728-135005833 | [ 2 ] 112505623-123755728 | [ 1 ] 101255518-112505623 | [ 2 ] 90005413-101255518 | [ 3 ] 78755308-90005413 | [ 2 ] 67505203-78755308 | [ 2 ] 56255098-67505203 | [ ] 45004993-56255098 | [ ] 33754888-45004993 | [ 1 ] 22504783-33754888 | [ 1 ] 11254678-22504783 | [ 1 ] 4573-11254678 |************************************************** [ 578 ] Storage Throughput = good ( 795.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023215 bp ( 40023215 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:50 (hh:mm:ss) Elapsed Time Round Time: 00:42:24 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11691 repeats masked totaling 2935254 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001260 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10001260 bp After Masking: 5464771 bp Masked: 45.36 % -- Input Database Coverage: 10001260 bp out of 3182923232 bp ( 0.31 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:09:31 (hh:mm:ss) Elapsed Time, 4078 HSPs Collected Number of families returned by RECON: 666 Round Time: 00:12:15 (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 : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37048 repeats masked totaling 9433300 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021950 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30021950 bp After Masking: 16513160 bp Masked: 45.00 % -- Input Database Coverage: 40023210 bp out of 3182923232 bp ( 1.26 % ) Sampling Time: 00:04:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 01:05:13 (hh:mm:ss) Elapsed Time, 23637 HSPs Collected Number of families returned by RECON: 2105 Round Time: 01:11:03 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123763 repeats masked totaling 30157227 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013713 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90013713 bp After Masking: 48314256 bp Masked: 46.33 % -- Input Database Coverage: 130036923 bp out of 3182923232 bp ( 4.09 % ) Sampling Time: 00:12:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:10:22 (hh:mm:ss) Elapsed Time, 105586 HSPs Collected Number of families returned by RECON: 7211 Round Time: 03:27:16 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 409409 repeats masked totaling 99839616 bp(s). - TE Masking time 00:07:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039549 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 270039549 bp After Masking: 136227877 bp Masked: 49.55 % -- Input Database Coverage: 400076472 bp out of 3182923232 bp ( 12.57 % ) Sampling Time: 00:37:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 16:52:20 (hh:mm:ss) Elapsed Time, 418603 HSPs Collected Number of families returned by RECON: 26621 Round Time: 17:48:28 (hh:mm:ss) Elapsed Time : 408 families discovered. RepeatScout/RECON discovery complete: 896 families found Classification Time: 00:45:54 (hh:mm:ss) Elapsed Time Program Time: 24:07:20 (hh:mm:ss) Elapsed Time