RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.sMnC0N/RM_833807.TueNov120837292024 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: 1731429447 Database = /scratch/tmp/rModeler.sMnC0N/GCA_037157525.1_mMolAlv2.hap1 - Sequences = 326 - Bases = 2478684717 - N50 = 116895412 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 260231772-278819313 | [ 1 ] 241644231-260231771 | [ ] 223056691-241644231 | [ ] 204469150-223056690 | [ ] 185881610-204469150 | [ ] 167294069-185881609 | [ ] 148706529-167294069 | [ 1 ] 130118988-148706528 | [ 2 ] 111531448-130118988 | [ 6 ] 92943907-111531447 | [ 4 ] 74356367-92943907 | [ 3 ] 55768826-74356366 | [ 4 ] 37181286-55768826 | [ 1 ] 18593745-37181285 | [ 1 ] 6205-18593745 |************************************************** [ 303 ] Storage Throughput = excellent ( 1630.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016855 bp ( 40016055 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:27 (hh:mm:ss) Elapsed Time Round Time: 00:12:22 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10790 repeats masked totaling 3073420 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033555 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10033455 bp After Masking: 6864443 bp Masked: 31.58 % -- Input Database Coverage: 10033555 bp out of 2478684717 bp ( 0.40 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 9401 HSPs Collected Number of families returned by RECON: 752 Round Time: 00:03:59 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36219 repeats masked totaling 9549418 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023371 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30022671 bp After Masking: 20076480 bp Masked: 33.13 % -- Input Database Coverage: 40056926 bp out of 2478684717 bp ( 1.62 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:16:40 (hh:mm:ss) Elapsed Time, 60349 HSPs Collected Number of families returned by RECON: 2279 Round Time: 00:18:46 (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 : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118380 repeats masked totaling 30736935 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029438 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90029038 bp After Masking: 58190000 bp Masked: 35.37 % -- Input Database Coverage: 130086364 bp out of 2478684717 bp ( 5.25 % ) Sampling Time: 00:05:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:10:12 (hh:mm:ss) Elapsed Time, 284120 HSPs Collected Number of families returned by RECON: 7213 Round Time: 01:16:57 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 384900 repeats masked totaling 98965100 bp(s). - TE Masking time 00:01:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015027 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 270014027 bp After Masking: 167287074 bp Masked: 38.05 % -- Input Database Coverage: 400101391 bp out of 2478684717 bp ( 16.14 % ) Sampling Time: 00:17:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 09:19:19 (hh:mm:ss) Elapsed Time, 1840615 HSPs Collected Number of families returned by RECON: 31451 Round Time: 09:47:10 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatScout/RECON discovery complete: 830 families found Classification Time: 00:18:10 (hh:mm:ss) Elapsed Time Program Time: 11:57:24 (hh:mm:ss) Elapsed Time