RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.mWL4qU/RM_1729206.TueNov191913402024 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: 1732072419 Database = /scratch/tmp/rModeler.mWL4qU/GCA_039720435.1_bAmaOch1.hap1 - Sequences = 1679 - Bases = 1361915838 - N50 = 95369017 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 129396336-138638134 | [ 2 ] 120154539-129396336 | [ 2 ] 110912741-120154538 | [ ] 101670944-110912741 | [ ] 92429147-101670944 | [ 2 ] 83187349-92429146 | [ 1 ] 73945552-83187349 | [ 1 ] 64703754-73945551 | [ ] 55461957-64703754 | [ ] 46220160-55461957 | [ 1 ] 36978362-46220159 | [ 1 ] 27736565-36978362 | [ 2 ] 18494767-27736564 | [ 4 ] 9252970-18494767 | [ 5 ] 11173-9252970 |************************************************** [ 1658 ] Storage Throughput = excellent ( 1160.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006469 bp ( 40005769 non ambiguous ) - Num Contigs Represented = 155 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:07 (hh:mm:ss) Elapsed Time Round Time: 00:11:29 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3435 repeats masked totaling 1276301 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020574 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10020474 bp After Masking: 7739044 bp Masked: 22.77 % -- Input Database Coverage: 10020574 bp out of 1361915838 bp ( 0.74 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 468 HSPs Collected Number of families returned by RECON: 179 Round Time: 00:03:52 (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 : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10340 repeats masked totaling 3789442 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025895 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 30025295 bp After Masking: 23323264 bp Masked: 22.32 % -- Input Database Coverage: 40046469 bp out of 1361915838 bp ( 2.94 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:14:29 (hh:mm:ss) Elapsed Time, 4620 HSPs Collected Number of families returned by RECON: 1026 Round Time: 00:17:43 (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 : 00:01:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33889 repeats masked totaling 11565558 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004920 bp Num Contigs Represented = 256 Non ambiguous bp: Initial: 90002020 bp After Masking: 70648458 bp Masked: 21.50 % -- Input Database Coverage: 130051389 bp out of 1361915838 bp ( 9.55 % ) Sampling Time: 00:07:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2648451 Comparison Time: 01:27:35 (hh:mm:ss) Elapsed Time, 43687 HSPs Collected Number of families returned by RECON: 6705 Round Time: 01:37:12 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116681 repeats masked totaling 40017740 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024758 bp Num Contigs Represented = 615 Non ambiguous bp: Initial: 270016158 bp After Masking: 203112349 bp Masked: 24.78 % -- Input Database Coverage: 400076147 bp out of 1361915838 bp ( 29.38 % ) Sampling Time: 00:22:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23670640 Comparison Time: 09:23:57 (hh:mm:ss) Elapsed Time, 202335 HSPs Collected Number of families returned by RECON: 42924 Round Time: 10:05:35 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 407 families found Classification Time: 00:27:40 (hh:mm:ss) Elapsed Time Program Time: 12:43:31 (hh:mm:ss) Elapsed Time