RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6p3tdI/RM_2895825.SatJul191237102025 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: 1752953828 Database = /dev/shm/rModeler.6p3tdI/GCA_048569135.1_fDirArg3.hap2 - Sequences = 4595 - Bases = 1884132620 - N50 = 4974830 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41376112-44331327 | [ 2 ] 38420898-41376112 | [ 1 ] 35465684-38420898 | [ 2 ] 32510469-35465683 | [ 4 ] 29555255-32510469 | [ 3 ] 26600041-29555255 | [ ] 23644827-26600041 | [ 4 ] 20689612-23644826 | [ ] 17734398-20689612 | [ 4 ] 14779184-17734398 | [ 5 ] 11823970-14779184 | [ 2 ] 8868755-11823969 | [ 9 ] 5913541-8868755 | [ 14 ] 2958327-5913541 | [ 28 ] 3113-2958327 |************************************************** [ 4517 ] Storage Throughput = excellent ( 1847.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016931 bp ( 40004531 non ambiguous ) - Num Contigs Represented = 512 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:23 (hh:mm:ss) Elapsed Time Round Time: 00:16:42 (hh:mm:ss) Elapsed Time : 923 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10299 repeats masked totaling 2565040 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009931 bp Num Contigs Represented = 175 Non ambiguous bp: Initial: 10006531 bp After Masking: 4609620 bp Masked: 53.93 % -- Input Database Coverage: 10009931 bp out of 1884132620 bp ( 0.53 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:02:39 (hh:mm:ss) Elapsed Time, 8841 HSPs Collected Number of families returned by RECON: 1430 Round Time: 00:05:44 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32718 repeats masked totaling 8058470 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046858 bp Num Contigs Represented = 412 Non ambiguous bp: Initial: 30037858 bp After Masking: 14502983 bp Masked: 51.72 % -- Input Database Coverage: 40056789 bp out of 1884132620 bp ( 2.13 % ) Sampling Time: 00:07:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 321201 Comparison Time: 00:10:21 (hh:mm:ss) Elapsed Time, 70379 HSPs Collected Number of families returned by RECON: 4929 Round Time: 00:18:54 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100160 repeats masked totaling 23471697 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048556 bp Num Contigs Represented = 907 Non ambiguous bp: Initial: 90016882 bp After Masking: 42054074 bp Masked: 53.28 % -- Input Database Coverage: 130105345 bp out of 1884132620 bp ( 6.91 % ) Sampling Time: 00:27:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2778903 Comparison Time: 00:50:04 (hh:mm:ss) Elapsed Time, 418839 HSPs Collected Number of families returned by RECON: 13567 Round Time: 01:22:25 (hh:mm:ss) Elapsed Time : 608 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:10:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 371851 repeats masked totaling 92036458 bp(s). - TE Masking time 00:05:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270128273 bp Num Contigs Represented = 1788 Non ambiguous bp: Initial: 270025481 bp After Masking: 107549325 bp Masked: 60.17 % -- Input Database Coverage: 400233618 bp out of 1884132620 bp ( 21.24 % ) Sampling Time: 01:16:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25222753 Comparison Time: 04:46:39 (hh:mm:ss) Elapsed Time, 1519462 HSPs Collected Number of families returned by RECON: 34221 Round Time: 06:31:47 (hh:mm:ss) Elapsed Time : 1819 families discovered. RepeatScout/RECON discovery complete: 3439 families found Classification Time: 01:40:08 (hh:mm:ss) Elapsed Time Program Time: 10:15:40 (hh:mm:ss) Elapsed Time