RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DFLVwb/RM_1659534.MonMar240630412025 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: 1742823039 Database = /dev/shm/rModeler.DFLVwb/GCA_965183815.1_bPlaLeu2.hap1.1 - Sequences = 669 - Bases = 1345843103 - N50 = 128451147 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 157946232-169228035 | [ 1 ] 146664430-157946232 | [ ] 135382628-146664430 | [ ] 124100825-135382627 | [ 3 ] 112819023-124100825 | [ ] 101537221-112819023 | [ 1 ] 90255418-101537220 | [ 1 ] 78973616-90255418 | [ 1 ] 67691814-78973616 | [ 1 ] 56410011-67691813 | [ 1 ] 45128209-56410011 | [ 2 ] 33846407-45128209 | [ ] 22564604-33846406 | [ 2 ] 11282802-22564604 | [ 5 ] 1000-11282802 |************************************************** [ 651 ] Storage Throughput = excellent ( 1844.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033905 bp ( 40030905 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:13 (hh:mm:ss) Elapsed Time Round Time: 00:10:23 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1875 repeats masked totaling 735066 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001743 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10000943 bp After Masking: 9074523 bp Masked: 9.26 % -- Input Database Coverage: 10001743 bp out of 1345843103 bp ( 0.74 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 2117 HSPs Collected Number of families returned by RECON: 261 Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4841 repeats masked totaling 1938563 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032082 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30029882 bp After Masking: 27106174 bp Masked: 9.74 % -- Input Database Coverage: 40033825 bp out of 1345843103 bp ( 2.97 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:14:46 (hh:mm:ss) Elapsed Time, 30338 HSPs Collected Number of families returned by RECON: 1590 Round Time: 00:16:37 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18251 repeats masked totaling 6722208 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035863 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 90027354 bp After Masking: 80618544 bp Masked: 10.45 % -- Input Database Coverage: 130069688 bp out of 1345843103 bp ( 9.66 % ) Sampling Time: 00:04:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:38:45 (hh:mm:ss) Elapsed Time, 208065 HSPs Collected Number of families returned by RECON: 8198 Round Time: 02:09:14 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66828 repeats masked totaling 25940839 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064267 bp Num Contigs Represented = 267 Non ambiguous bp: Initial: 270035720 bp After Masking: 235763858 bp Masked: 12.69 % -- Input Database Coverage: 400133955 bp out of 1345843103 bp ( 29.73 % ) Sampling Time: 00:14:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23218705 Comparison Time: 11:32:25 (hh:mm:ss) Elapsed Time, 940620 HSPs Collected Number of families returned by RECON: 52511 Round Time: 12:03:19 (hh:mm:ss) Elapsed Time : 277 families discovered. RepeatScout/RECON discovery complete: 448 families found Classification Time: 00:21:19 (hh:mm:ss) Elapsed Time Program Time: 15:04:35 (hh:mm:ss) Elapsed Time