RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.zGvSH0/RM_225908.SatApr191901162025 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: 1745114475 Database = /data/tmp/rModeler.zGvSH0/GCF_030463535.1_fSalBra1.hap2 - Sequences = 103 - Bases = 1066483687 - N50 = 41637409 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 92763668-99388286 | [ 1 ] 86139051-92763668 | [ ] 79514433-86139050 | [ ] 72889816-79514433 | [ ] 66265199-72889816 | [ ] 59640581-66265198 | [ 1 ] 53015964-59640581 | [ ] 46391346-53015963 |** [ 4 ] 39766729-46391346 |*** [ 6 ] 33142112-39766729 |****** [ 10 ] 26517494-33142111 |* [ 3 ] 19892877-26517494 | [ ] 13268259-19892876 | [ ] 6643642-13268259 | [ ] 19025-6643642 |************************************************** [ 78 ] Storage Throughput = good ( 806.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40473881 bp ( 40022259 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:00 (hh:mm:ss) Elapsed Time Round Time: 00:25:30 (hh:mm:ss) Elapsed Time : 728 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15672 repeats masked totaling 2359551 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120705 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10003699 bp After Masking: 6602562 bp Masked: 34.00 % -- Input Database Coverage: 10120705 bp out of 1066483687 bp ( 0.95 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:08 (hh:mm:ss) Elapsed Time, 10777 HSPs Collected Number of families returned by RECON: 1517 Round Time: 00:09:47 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47571 repeats masked totaling 7245746 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30353153 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30018537 bp After Masking: 19319550 bp Masked: 35.64 % -- Input Database Coverage: 40473858 bp out of 1066483687 bp ( 3.80 % ) Sampling Time: 00:06:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:25:53 (hh:mm:ss) Elapsed Time, 71485 HSPs Collected Number of families returned by RECON: 5673 Round Time: 00:52:08 (hh:mm:ss) Elapsed Time : 148 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164834 repeats masked totaling 24750922 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90910615 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90021930 bp After Masking: 54868803 bp Masked: 39.05 % -- Input Database Coverage: 131384473 bp out of 1066483687 bp ( 12.32 % ) Sampling Time: 00:18:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 02:35:23 (hh:mm:ss) Elapsed Time, 339823 HSPs Collected Number of families returned by RECON: 17512 Round Time: 03:37:52 (hh:mm:ss) Elapsed Time : 479 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 573239 repeats masked totaling 87004750 bp(s). - TE Masking time 00:10:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271921232 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 270004226 bp After Masking: 153110918 bp Masked: 43.29 % -- Input Database Coverage: 403305705 bp out of 1066483687 bp ( 37.82 % ) Sampling Time: 00:59:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 19:57:45 (hh:mm:ss) Elapsed Time, 943418 HSPs Collected Number of families returned by RECON: 54634 Round Time: 24:50:20 (hh:mm:ss) Elapsed Time : 1077 families discovered. RepeatScout/RECON discovery complete: 2454 families found Classification Time: 01:39:34 (hh:mm:ss) Elapsed Time Program Time: 31:35:11 (hh:mm:ss) Elapsed Time