RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.piSf7V/RM_338962.TueNov191928112024 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: 1732073290 Database = /scratch/tmp/rModeler.piSf7V/GCA_029633855.2_fHopMal1.hap1 - Sequences = 597 - Bases = 1186354877 - N50 = 57277341 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84911242-90976188 | [ 3 ] 78846296-84911241 | [ 1 ] 72781350-78846295 | [ 1 ] 66716404-72781349 | [ ] 60651458-66716403 | [ ] 54586512-60651457 | [ 2 ] 48521566-54586511 | [ 1 ] 42456621-48521566 | [ 4 ] 36391675-42456620 | [ 7 ] 30326729-36391674 | [ 1 ] 24261783-30326728 | [ 1 ] 18196837-24261782 | [ ] 12131891-18196836 | [ ] 6066945-12131890 | [ ] 2000-6066945 |************************************************** [ 576 ] Storage Throughput = excellent ( 1648.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42657900 bp ( 40005038 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:06 (hh:mm:ss) Elapsed Time Round Time: 00:13:29 (hh:mm:ss) Elapsed Time : 607 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15612 repeats masked totaling 2365365 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10864722 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10004583 bp After Masking: 6546561 bp Masked: 34.56 % -- Input Database Coverage: 10864722 bp out of 1186354877 bp ( 0.92 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37128 Comparison Time: 00:03:13 (hh:mm:ss) Elapsed Time, 55392 HSPs Collected Number of families returned by RECON: 1313 Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52670 repeats masked totaling 7550107 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31793098 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30000375 bp After Masking: 19488642 bp Masked: 35.04 % -- Input Database Coverage: 42657820 bp out of 1186354877 bp ( 3.60 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 318801 Comparison Time: 00:14:35 (hh:mm:ss) Elapsed Time, 151082 HSPs Collected Number of families returned by RECON: 4996 Round Time: 00:18:16 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163470 repeats masked totaling 23797901 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95048389 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90003469 bp After Masking: 56601988 bp Masked: 37.11 % -- Input Database Coverage: 137706209 bp out of 1186354877 bp ( 11.61 % ) Sampling Time: 00:09:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2866815 Comparison Time: 01:24:33 (hh:mm:ss) Elapsed Time, 846122 HSPs Collected Number of families returned by RECON: 15182 Round Time: 01:40:39 (hh:mm:ss) Elapsed Time : 459 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 575526 repeats masked totaling 86673783 bp(s). - TE Masking time 00:03:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 286512630 bp Num Contigs Represented = 248 Non ambiguous bp: Initial: 270024028 bp After Masking: 155267996 bp Masked: 42.50 % -- Input Database Coverage: 424218839 bp out of 1186354877 bp ( 35.76 % ) Sampling Time: 00:29:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26089476 Comparison Time: 09:09:07 (hh:mm:ss) Elapsed Time, 8664941 HSPs Collected Number of families returned by RECON: 48904 Round Time: 10:19:07 (hh:mm:ss) Elapsed Time : 984 families discovered. RepeatScout/RECON discovery complete: 2180 families found Classification Time: 00:50:34 (hh:mm:ss) Elapsed Time Program Time: 13:26:44 (hh:mm:ss) Elapsed Time