RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.cq6mDe/RM_176104.ThuNov141156072024 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: 1731614166 Database = /scratch/tmp/rModeler.cq6mDe/GCA_964263955.1_fCorLav1.hap1.1 - Sequences = 11150 - Bases = 2842862595 - N50 = 47886639 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 89193571-95564469 | [ 1 ] 82822673-89193570 | [ 1 ] 76451775-82822672 | [ 3 ] 70080877-76451774 | [ ] 63709979-70080876 | [ 2 ] 57339081-63709978 | [ 5 ] 50968183-57339080 | [ 4 ] 44597285-50968182 | [ 11 ] 38226387-44597284 | [ 7 ] 31855489-38226386 | [ 4 ] 25484591-31855488 | [ ] 19113693-25484590 | [ 1 ] 12742795-19113692 | [ 1 ] 6371897-12742794 | [ 1 ] 1000-6371897 |************************************************** [ 11109 ] Storage Throughput = excellent ( 1458.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038325 bp ( 40021525 non ambiguous ) - Num Contigs Represented = 387 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:04 (hh:mm:ss) Elapsed Time Round Time: 00:12:12 (hh:mm:ss) Elapsed Time : 907 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15390 repeats masked totaling 4764877 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005316 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 10001716 bp After Masking: 3894962 bp Masked: 61.06 % -- Input Database Coverage: 10005316 bp out of 2842862595 bp ( 0.35 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 6165 HSPs Collected Number of families returned by RECON: 1037 Round Time: 00:04:46 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44364 repeats masked totaling 14010259 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033006 bp Num Contigs Represented = 304 Non ambiguous bp: Initial: 30019806 bp After Masking: 11426161 bp Masked: 61.94 % -- Input Database Coverage: 40038322 bp out of 2842862595 bp ( 1.41 % ) Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 335790 Comparison Time: 00:10:12 (hh:mm:ss) Elapsed Time, 38190 HSPs Collected Number of families returned by RECON: 3323 Round Time: 00:16:35 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135177 repeats masked totaling 41501722 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90071640 bp Num Contigs Represented = 757 Non ambiguous bp: Initial: 90034435 bp After Masking: 34710794 bp Masked: 61.45 % -- Input Database Coverage: 130109962 bp out of 2842862595 bp ( 4.58 % ) Sampling Time: 00:16:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2973141 Comparison Time: 00:51:43 (hh:mm:ss) Elapsed Time, 293484 HSPs Collected Number of families returned by RECON: 9639 Round Time: 01:12:30 (hh:mm:ss) Elapsed Time : 509 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465638 repeats masked totaling 140082845 bp(s). - TE Masking time 00:04:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270117915 bp Num Contigs Represented = 2038 Non ambiguous bp: Initial: 270002016 bp After Masking: 89400460 bp Masked: 66.89 % -- Input Database Coverage: 400227877 bp out of 2842862595 bp ( 14.08 % ) Sampling Time: 00:48:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26743641 Comparison Time: 05:27:49 (hh:mm:ss) Elapsed Time, 820975 HSPs Collected Number of families returned by RECON: 30852 Round Time: 06:33:47 (hh:mm:ss) Elapsed Time : 1022 families discovered. RepeatScout/RECON discovery complete: 2517 families found Classification Time: 00:53:15 (hh:mm:ss) Elapsed Time Program Time: 09:13:05 (hh:mm:ss) Elapsed Time