RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mcdMpK/RM_17736.MonDec41240142023 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: 1701722413 Database = /dev/shm/rModeler.mcdMpK/GCA_031021085.1_rEryReg1.hap2 - Sequences = 1128 - Bases = 2038227610 - N50 = 4311569 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 16162564-17315906 | [ 2 ] 15009223-16162564 | [ 1 ] 13855881-15009222 | [ 3 ] 12702540-13855881 | [ 2 ] 11549198-12702539 | [ 6 ] 10395857-11549198 | [ 9 ] 9242515-10395856 | [ 10 ] 8089174-9242515 | [ 11 ] 6935832-8089173 |* [ 16 ] 5782491-6935832 |* [ 25 ] 4629149-5782490 |** [ 35 ] 3475808-4629149 |**** [ 67 ] 2322466-3475807 |****** [ 91 ] 1169125-2322466 |*********** [ 163 ] 15784-1169125 |************************************************** [ 687 ] Storage Throughput = excellent ( 1144.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023912 bp ( 40023912 non ambiguous ) - Num Contigs Represented = 452 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:49 (hh:mm:ss) Elapsed Time Round Time: 00:34:50 (hh:mm:ss) Elapsed Time : 702 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21084 repeats masked totaling 4691675 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019986 bp Num Contigs Represented = 191 Non ambiguous bp: Initial: 10019986 bp After Masking: 4747724 bp Masked: 52.62 % -- Input Database Coverage: 10019986 bp out of 2038227610 bp ( 0.49 % ) Sampling Time: 00:02:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 6213 HSPs Collected Number of families returned by RECON: 906 Round Time: 00:08:50 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61861 repeats masked totaling 14279778 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003866 bp Num Contigs Represented = 387 Non ambiguous bp: Initial: 30003866 bp After Masking: 14153477 bp Masked: 52.83 % -- Input Database Coverage: 40023852 bp out of 2038227610 bp ( 1.96 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:25:16 (hh:mm:ss) Elapsed Time, 32427 HSPs Collected Number of families returned by RECON: 3002 Round Time: 00:30:40 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 199325 repeats masked totaling 44064274 bp(s). - TE Masking time 00:03:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017538 bp Num Contigs Represented = 668 Non ambiguous bp: Initial: 90017538 bp After Masking: 41288530 bp Masked: 54.13 % -- Input Database Coverage: 130041390 bp out of 2038227610 bp ( 6.38 % ) Sampling Time: 00:12:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 02:35:36 (hh:mm:ss) Elapsed Time, 192489 HSPs Collected Number of families returned by RECON: 9061 Round Time: 02:54:51 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 644512 repeats masked totaling 140924462 bp(s). - TE Masking time 00:13:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018395 bp Num Contigs Represented = 904 Non ambiguous bp: Initial: 270018395 bp After Masking: 115046393 bp Masked: 57.39 % -- Input Database Coverage: 400059785 bp out of 2038227610 bp ( 19.63 % ) Sampling Time: 00:47:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 18:41:00 (hh:mm:ss) Elapsed Time, 668180 HSPs Collected Number of families returned by RECON: 27555 Round Time: 20:10:28 (hh:mm:ss) Elapsed Time : 948 families discovered. RepeatScout/RECON discovery complete: 2108 families found Classification Time: 01:21:50 (hh:mm:ss) Elapsed Time Program Time: 25:41:29 (hh:mm:ss) Elapsed Time