RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ikN3AI/RM_765746.MonApr211255422025 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: 1745265340 Database = /dev/shm/rModeler.ikN3AI/GCA_965231335.1_bBraCan1.1 - Sequences = 614 - Bases = 1311899232 - N50 = 89450475 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 199416374-213660330 | [ 1 ] 185172419-199416374 | [ ] 170928464-185172419 | [ ] 156684508-170928463 | [ 1 ] 142440553-156684508 | [ ] 128196598-142440553 | [ ] 113952642-128196597 | [ 1 ] 99708687-113952642 | [ ] 85464732-99708687 | [ 1 ] 71220776-85464731 | [ 1 ] 56976821-71220776 | [ 1 ] 42732866-56976821 | [ ] 28488910-42732865 | [ 3 ] 14244955-28488910 | [ 10 ] 1000-14244955 |************************************************** [ 595 ] Storage Throughput = excellent ( 1658.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028507 bp ( 40026307 non ambiguous ) - Num Contigs Represented = 126 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:49 (hh:mm:ss) Elapsed Time Round Time: 00:12:18 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (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... 1682 repeats masked totaling 801269 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011601 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10011001 bp After Masking: 8342117 bp Masked: 16.67 % -- Input Database Coverage: 10011601 bp out of 1311899232 bp ( 0.76 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 301 HSPs Collected Number of families returned by RECON: 182 Round Time: 00:04:35 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5187 repeats masked totaling 2462890 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016826 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 30015226 bp After Masking: 24294543 bp Masked: 19.06 % -- Input Database Coverage: 40028427 bp out of 1311899232 bp ( 3.05 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:14:01 (hh:mm:ss) Elapsed Time, 6169 HSPs Collected Number of families returned by RECON: 1178 Round Time: 00:17:42 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16588 repeats masked totaling 7792964 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011381 bp Num Contigs Represented = 184 Non ambiguous bp: Initial: 90002981 bp After Masking: 72634941 bp Masked: 19.30 % -- Input Database Coverage: 130039808 bp out of 1311899232 bp ( 9.91 % ) Sampling Time: 00:10:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 01:31:05 (hh:mm:ss) Elapsed Time, 100264 HSPs Collected Number of families returned by RECON: 7378 Round Time: 01:43:08 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58010 repeats masked totaling 24925332 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056357 bp Num Contigs Represented = 329 Non ambiguous bp: Initial: 270034258 bp After Masking: 216828930 bp Masked: 19.70 % -- Input Database Coverage: 400096165 bp out of 1311899232 bp ( 30.50 % ) Sampling Time: 00:29:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 11:29:48 (hh:mm:ss) Elapsed Time, 812354 HSPs Collected Number of families returned by RECON: 47991 Round Time: 12:12:51 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatScout/RECON discovery complete: 308 families found Classification Time: 00:14:04 (hh:mm:ss) Elapsed Time Program Time: 14:44:38 (hh:mm:ss) Elapsed Time