RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.d99DCi/RM_2698557.MonApr211255432025 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: 1745265343 Database = /dev/shm/rModeler.d99DCi/GCA_965231275.1_bZosLat1.hap1.1 - Sequences = 427 - Bases = 1143512649 - N50 = 74552497 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 143499172-153749042 | [ 1 ] 133249303-143499172 | [ ] 122999433-133249302 | [ ] 112749564-122999433 | [ 2 ] 102499694-112749563 | [ ] 92249825-102499694 | [ ] 81999955-92249824 | [ 1 ] 71750086-81999955 | [ 2 ] 61500216-71750085 | [ ] 51250347-61500216 | [ 1 ] 41000477-51250346 | [ ] 30750608-41000477 | [ 4 ] 20500738-30750607 | [ 4 ] 10250869-20500738 | [ 7 ] 1000-10250869 |************************************************** [ 405 ] Storage Throughput = excellent ( 1663.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027965 bp ( 40025069 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:25 (hh:mm:ss) Elapsed Time Round Time: 00:10:23 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2872 repeats masked totaling 1011980 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012536 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10012136 bp After Masking: 8705865 bp Masked: 13.05 % -- Input Database Coverage: 10012536 bp out of 1143512649 bp ( 0.88 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 866 HSPs Collected Number of families returned by RECON: 380 Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (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... 9152 repeats masked totaling 3019479 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015408 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30012912 bp After Masking: 26022875 bp Masked: 13.29 % -- Input Database Coverage: 40027944 bp out of 1143512649 bp ( 3.50 % ) Sampling Time: 00:01:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:16:21 (hh:mm:ss) Elapsed Time, 13343 HSPs Collected Number of families returned by RECON: 2053 Round Time: 00:18:24 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27830 repeats masked totaling 8269581 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019426 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 90009415 bp After Masking: 79063602 bp Masked: 12.16 % -- Input Database Coverage: 130047370 bp out of 1143512649 bp ( 11.37 % ) Sampling Time: 00:05:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 01:52:20 (hh:mm:ss) Elapsed Time, 100470 HSPs Collected Number of families returned by RECON: 11987 Round Time: 02:01:59 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93082 repeats masked totaling 29328278 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069229 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 270034170 bp After Masking: 232026693 bp Masked: 14.08 % -- Input Database Coverage: 400116599 bp out of 1143512649 bp ( 34.99 % ) Sampling Time: 00:32:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 14:00:46 (hh:mm:ss) Elapsed Time, 935046 HSPs Collected Number of families returned by RECON: 72840 Round Time: 14:58:59 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatScout/RECON discovery complete: 623 families found Classification Time: 00:22:30 (hh:mm:ss) Elapsed Time Program Time: 17:56:06 (hh:mm:ss) Elapsed Time