RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.iaY3MS/RM_83524.WedJan110802542023 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: 1673452972 Database = /dev/shm/rModeler.iaY3MS/GCF_025201925.1_rGopFla2.mat.asm - Sequences = 621 - Bases = 2460542086 - N50 = 288984084 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 355130324-380496693 | [ 1 ] 329763956-355130324 | [ ] 304397588-329763956 | [ ] 279031220-304397588 | [ 2 ] 253664852-279031220 | [ ] 228298484-253664852 | [ ] 202932116-228298484 | [ 1 ] 177565747-202932115 | [ ] 152199379-177565747 | [ 1 ] 126833011-152199379 | [ 1 ] 101466643-126833011 | [ 2 ] 76100275-101466643 | [ 2 ] 50733907-76100275 | [ 2 ] 25367539-50733907 | [ 8 ] 1171-25367539 |************************************************** [ 601 ] Storage Throughput = excellent ( 1546.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41787868 bp ( 40012980 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:20 (hh:mm:ss) Elapsed Time Round Time: 00:23:51 (hh:mm:ss) Elapsed Time : 522 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12669 repeats masked totaling 3264717 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10410659 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10038512 bp After Masking: 6524289 bp Masked: 35.01 % -- Input Database Coverage: 10410659 bp out of 2460542086 bp ( 0.42 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 12613 HSPs Collected Number of families returned by RECON: 1556 Round Time: 00:08:23 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42524 repeats masked totaling 10815854 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31417056 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30014315 bp After Masking: 18383211 bp Masked: 38.75 % -- Input Database Coverage: 41827715 bp out of 2460542086 bp ( 1.70 % ) Sampling Time: 00:04:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 311655 Comparison Time: 00:24:15 (hh:mm:ss) Elapsed Time, 62518 HSPs Collected Number of families returned by RECON: 4444 Round Time: 00:30:05 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143640 repeats masked totaling 34536297 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 93710884 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 90008985 bp After Masking: 53033775 bp Masked: 41.08 % -- Input Database Coverage: 135538599 bp out of 2460542086 bp ( 5.51 % ) Sampling Time: 00:12:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2774190 Comparison Time: 01:59:10 (hh:mm:ss) Elapsed Time, 227299 HSPs Collected Number of families returned by RECON: 12726 Round Time: 02:18:14 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:31:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 493244 repeats masked totaling 116604502 bp(s). - TE Masking time 00:06:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 279496007 bp Num Contigs Represented = 190 Non ambiguous bp: Initial: 270027024 bp After Masking: 145748786 bp Masked: 46.02 % -- Input Database Coverage: 415034606 bp out of 2460542086 bp ( 16.87 % ) Sampling Time: 00:58:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24594591 Comparison Time: 12:56:03 (hh:mm:ss) Elapsed Time, 534599 HSPs Collected Number of families returned by RECON: 40014 Round Time: 14:36:59 (hh:mm:ss) Elapsed Time : 982 families discovered. RepeatScout/RECON discovery complete: 2063 families found Classification Time: 01:00:23 (hh:mm:ss) Elapsed Time Program Time: 18:57:55 (hh:mm:ss) Elapsed Time