RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.X85BNE/RM_8060.SunDec81839092024 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: 1733711948 Database = /scratch/tmp/rModeler.X85BNE/GCA_039720425.1_bAmaOch1.hap2 - Sequences = 2468 - Bases = 1356986306 - N50 = 92530657 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 129654946-138915110 | [ 2 ] 120394782-129654945 | [ 1 ] 111134619-120394782 | [ ] 101874455-111134618 | [ ] 92614292-101874455 | [ 1 ] 83354128-92614291 | [ 2 ] 74093964-83354127 | [ 1 ] 64833801-74093964 | [ ] 55573637-64833800 | [ ] 46313474-55573637 | [ ] 37053310-46313473 | [ 2 ] 27793146-37053309 | [ 1 ] 18532983-27793146 | [ 4 ] 9272819-18532982 | [ 5 ] 12656-9272819 |************************************************** [ 2449 ] Storage Throughput = fair ( 610.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008930 bp ( 40008430 non ambiguous ) - Num Contigs Represented = 234 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:40 (hh:mm:ss) Elapsed Time Round Time: 00:41:33 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3371 repeats masked totaling 1041439 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007445 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 10007145 bp After Masking: 7322729 bp Masked: 26.82 % -- Input Database Coverage: 10007445 bp out of 1356986306 bp ( 0.74 % ) Sampling Time: 00:02:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 527 HSPs Collected Number of families returned by RECON: 163 Round Time: 00:07:19 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9935 repeats masked totaling 3278719 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001444 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 30001244 bp After Masking: 21044957 bp Masked: 29.85 % -- Input Database Coverage: 40008889 bp out of 1356986306 bp ( 2.95 % ) Sampling Time: 00:08:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 298378 Comparison Time: 00:26:59 (hh:mm:ss) Elapsed Time, 7094 HSPs Collected Number of families returned by RECON: 934 Round Time: 00:35:45 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31448 repeats masked totaling 9857955 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011821 bp Num Contigs Represented = 501 Non ambiguous bp: Initial: 90010421 bp After Masking: 62875325 bp Masked: 30.15 % -- Input Database Coverage: 130020710 bp out of 1356986306 bp ( 9.58 % ) Sampling Time: 00:24:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2736630 Comparison Time: 03:12:01 (hh:mm:ss) Elapsed Time, 38309 HSPs Collected Number of families returned by RECON: 5558 Round Time: 03:45:21 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:58:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101869 repeats masked totaling 33847239 bp(s). - TE Masking time 00:04:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012359 bp Num Contigs Represented = 1159 Non ambiguous bp: Initial: 270005959 bp After Masking: 184218705 bp Masked: 31.77 % -- Input Database Coverage: 400033069 bp out of 1356986306 bp ( 29.48 % ) Sampling Time: 01:13:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24426555 Comparison Time: 25:55:09 (hh:mm:ss) Elapsed Time, 147366 HSPs Collected Number of families returned by RECON: 36982 Round Time: 27:46:09 (hh:mm:ss) Elapsed Time : 187 families discovered. RepeatScout/RECON discovery complete: 345 families found Classification Time: 00:41:38 (hh:mm:ss) Elapsed Time Program Time: 33:37:45 (hh:mm:ss) Elapsed Time