RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.gIgPjC/RM_2948104.ThuNov141320362024 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: 1731619235 Database = /scratch/tmp/rModeler.gIgPjC/GCA_964195595.1_bCalBor7.hap1.1 - Sequences = 355 - Bases = 1366205003 - N50 = 87715099 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206368189-221108703 | [ 1 ] 191627675-206368188 | [ ] 176887162-191627675 | [ ] 162146648-176887161 | [ 1 ] 147406135-162146648 | [ ] 132665621-147406134 | [ ] 117925108-132665621 | [ 1 ] 103184594-117925107 | [ ] 88444081-103184594 | [ ] 73703567-88444080 | [ 2 ] 58963054-73703567 | [ ] 44222540-58963053 | [ 4 ] 29482027-44222540 | [ 2 ] 14741513-29482026 |* [ 11 ] 1000-14741513 |************************************************** [ 333 ] Storage Throughput = excellent ( 1536.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006415 bp ( 40003615 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:11 (hh:mm:ss) Elapsed Time Round Time: 00:10:51 (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 : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1405 repeats masked totaling 821088 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014560 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10014560 bp After Masking: 8710707 bp Masked: 13.02 % -- Input Database Coverage: 10014560 bp out of 1366205003 bp ( 0.73 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 587 HSPs Collected Number of families returned by RECON: 215 Round Time: 00:04:06 (hh:mm:ss) Elapsed Time : 1 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 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6117 repeats masked totaling 2753504 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031749 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30028949 bp After Masking: 25990601 bp Masked: 13.45 % -- Input Database Coverage: 40046309 bp out of 1366205003 bp ( 2.93 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:14:35 (hh:mm:ss) Elapsed Time, 24893 HSPs Collected Number of families returned by RECON: 1504 Round Time: 00:17:16 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16907 repeats masked totaling 7627745 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032725 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90025325 bp After Masking: 78924517 bp Masked: 12.33 % -- Input Database Coverage: 130079034 bp out of 1366205003 bp ( 9.52 % ) Sampling Time: 00:07:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:29:56 (hh:mm:ss) Elapsed Time, 54984 HSPs Collected Number of families returned by RECON: 7905 Round Time: 01:39:34 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72789 repeats masked totaling 29654983 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037807 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 270016807 bp After Masking: 229520619 bp Masked: 15.00 % -- Input Database Coverage: 400116841 bp out of 1366205003 bp ( 29.29 % ) Sampling Time: 00:22:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 11:19:29 (hh:mm:ss) Elapsed Time, 374649 HSPs Collected Number of families returned by RECON: 47339 Round Time: 12:21:07 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatScout/RECON discovery complete: 440 families found Classification Time: 00:19:48 (hh:mm:ss) Elapsed Time Program Time: 14:52:42 (hh:mm:ss) Elapsed Time