RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CX7nza/RM_2621293.ThuApr101848362025 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: 1744336116 Database = /dev/shm/rModeler.CX7nza/GCF_963455315.2_mGloMel1.2 - Sequences = 992 - Bases = 2651276051 - N50 = 108122213 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 175565434-188105751 | [ 2 ] 163025117-175565433 | [ 1 ] 150484800-163025116 | [ ] 137944484-150484800 | [ 2 ] 125404167-137944483 | [ 1 ] 112863850-125404166 | [ 2 ] 100323533-112863849 | [ 4 ] 87783217-100323533 | [ 3 ] 75242900-87783216 | [ 4 ] 62702583-75242899 | [ 1 ] 50162266-62702582 | [ 1 ] 37621950-50162266 | [ ] 25081633-37621949 | [ 1 ] 12541316-25081632 | [ ] 1000-12541316 |************************************************** [ 970 ] Storage Throughput = excellent ( 1729.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031162 bp ( 40027562 non ambiguous ) - Num Contigs Represented = 133 - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:51 (hh:mm:ss) Elapsed Time Round Time: 00:16:53 (hh:mm:ss) Elapsed Time : 184 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 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9685 repeats masked totaling 2795476 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004640 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10003640 bp After Masking: 6934200 bp Masked: 30.68 % -- Input Database Coverage: 10004640 bp out of 2651276051 bp ( 0.38 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 65778 HSPs Collected Number of families returned by RECON: 829 Round Time: 00:04:29 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34521 repeats masked totaling 9761405 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026520 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 30023920 bp After Masking: 18953776 bp Masked: 36.87 % -- Input Database Coverage: 40031160 bp out of 2651276051 bp ( 1.51 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:13:02 (hh:mm:ss) Elapsed Time, 52203 HSPs Collected Number of families returned by RECON: 2386 Round Time: 00:15:57 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114578 repeats masked totaling 32022032 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012761 bp Num Contigs Represented = 209 Non ambiguous bp: Initial: 90004102 bp After Masking: 54975288 bp Masked: 38.92 % -- Input Database Coverage: 130043921 bp out of 2651276051 bp ( 4.90 % ) Sampling Time: 00:06:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:12:59 (hh:mm:ss) Elapsed Time, 254694 HSPs Collected Number of families returned by RECON: 8074 Round Time: 01:20:45 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383463 repeats masked totaling 104869868 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046276 bp Num Contigs Represented = 410 Non ambiguous bp: Initial: 270024651 bp After Masking: 156093155 bp Masked: 42.19 % -- Input Database Coverage: 400090197 bp out of 2651276051 bp ( 15.09 % ) Sampling Time: 00:19:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 08:09:04 (hh:mm:ss) Elapsed Time, 3189899 HSPs Collected Number of families returned by RECON: 30933 Round Time: 08:37:12 (hh:mm:ss) Elapsed Time : 296 families discovered. RepeatScout/RECON discovery complete: 736 families found Classification Time: 00:14:08 (hh:mm:ss) Elapsed Time Program Time: 10:49:24 (hh:mm:ss) Elapsed Time