RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.h2vPpg/RM_2445.FriDec61329092024 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: 1733520548 Database = /scratch/tmp/rModeler.h2vPpg/GCA_037176705.1_mMolAlv2.hap2 - Sequences = 287 - Bases = 2504806577 - N50 = 116429828 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 258111611-276547744 | [ 1 ] 239675478-258111610 | [ ] 221239346-239675478 | [ ] 202803213-221239345 | [ ] 184367081-202803213 | [ ] 165930948-184367080 | [ ] 147494816-165930948 | [ 1 ] 129058683-147494815 | [ 2 ] 110622551-129058683 |* [ 6 ] 92186418-110622550 | [ 4 ] 73750286-92186418 | [ 3 ] 55314153-73750285 | [ 4 ] 36878021-55314153 | [ 1 ] 18441888-36878020 | [ 1 ] 5756-18441888 |************************************************** [ 264 ] Storage Throughput = fair ( 594.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002175 bp ( 40001775 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:08 (hh:mm:ss) Elapsed Time Round Time: 00:31:07 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11191 repeats masked totaling 3165122 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001441 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10001241 bp After Masking: 6691535 bp Masked: 33.09 % -- Input Database Coverage: 10001441 bp out of 2504806577 bp ( 0.40 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 8092 HSPs Collected Number of families returned by RECON: 714 Round Time: 00:07:25 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39773 repeats masked totaling 9582120 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000654 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30000454 bp After Masking: 19997705 bp Masked: 33.34 % -- Input Database Coverage: 40002095 bp out of 2504806577 bp ( 1.60 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:18 (hh:mm:ss) Elapsed Time, 34922 HSPs Collected Number of families returned by RECON: 2121 Round Time: 00:37:33 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125311 repeats masked totaling 33435582 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014581 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90014381 bp After Masking: 55299036 bp Masked: 38.57 % -- Input Database Coverage: 130016676 bp out of 2504806577 bp ( 5.19 % ) Sampling Time: 00:11:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:24:03 (hh:mm:ss) Elapsed Time, 95765 HSPs Collected Number of families returned by RECON: 7090 Round Time: 03:43:51 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 413266 repeats masked totaling 107605798 bp(s). - TE Masking time 00:07:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036602 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 270035202 bp After Masking: 158815287 bp Masked: 41.19 % -- Input Database Coverage: 400053278 bp out of 2504806577 bp ( 15.97 % ) Sampling Time: 00:36:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 24:11:59 (hh:mm:ss) Elapsed Time, 248474 HSPs Collected Number of families returned by RECON: 28777 Round Time: 25:28:36 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatScout/RECON discovery complete: 792 families found Classification Time: 00:40:42 (hh:mm:ss) Elapsed Time Program Time: 31:09:14 (hh:mm:ss) Elapsed Time