RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.6PiHnB/RM_3824733.MonDec21730062024 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: 1733189405 Database = /scratch/tmp/rModeler.6PiHnB/GCF_029633855.1_fHopMal1.hap1 - Sequences = 598 - Bases = 1186371479 - 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 |************************************************** [ 577 ] Storage Throughput = excellent ( 1474.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42359869 bp ( 40037043 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:33 (hh:mm:ss) Elapsed Time Round Time: 00:15:09 (hh:mm:ss) Elapsed Time : 562 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15290 repeats masked totaling 2271671 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10654504 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10023995 bp After Masking: 6725545 bp Masked: 32.91 % -- Input Database Coverage: 10654504 bp out of 1186371479 bp ( 0.90 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36046 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 21035 HSPs Collected Number of families returned by RECON: 1509 Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49681 repeats masked totaling 7296293 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31705360 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30013043 bp After Masking: 19814984 bp Masked: 33.98 % -- Input Database Coverage: 42359864 bp out of 1186371479 bp ( 3.57 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 316410 Comparison Time: 00:14:47 (hh:mm:ss) Elapsed Time, 143650 HSPs Collected Number of families returned by RECON: 4745 Round Time: 00:18:55 (hh:mm:ss) Elapsed Time : 127 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 160658 repeats masked totaling 24308018 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94812303 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 90029755 bp After Masking: 56837017 bp Masked: 36.87 % -- Input Database Coverage: 137172167 bp out of 1186371479 bp ( 11.56 % ) Sampling Time: 00:09:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2888406 Comparison Time: 01:25:05 (hh:mm:ss) Elapsed Time, 1037903 HSPs Collected Number of families returned by RECON: 15339 Round Time: 01:40:29 (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 : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 567524 repeats masked totaling 86508353 bp(s). - TE Masking time 00:04:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 285295305 bp Num Contigs Represented = 250 Non ambiguous bp: Initial: 270015743 bp After Masking: 154940399 bp Masked: 42.62 % -- Input Database Coverage: 422467472 bp out of 1186371479 bp ( 35.61 % ) Sampling Time: 00:30:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25894806 Comparison Time: 09:45:33 (hh:mm:ss) Elapsed Time, 7106081 HSPs Collected Number of families returned by RECON: 50869 Round Time: 10:48:33 (hh:mm:ss) Elapsed Time : 973 families discovered. RepeatScout/RECON discovery complete: 2157 families found Classification Time: 00:48:38 (hh:mm:ss) Elapsed Time Program Time: 13:56:10 (hh:mm:ss) Elapsed Time