RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PMPB3z/RM_44783.SunJan80405442023 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: 1673179543 Database = /dev/shm/rModeler.PMPB3z/GCA_020746105.1_bTroSur1.pri.cur - Sequences = 182 - Bases = 1165749515 - N50 = 87900276 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207400240-222214447 | [ 1 ] 192586033-207400239 | [ ] 177771827-192586033 | [ ] 162957620-177771826 | [ ] 148143414-162957620 | [ ] 133329207-148143413 | [ ] 118515001-133329207 | [ 1 ] 103700794-118515000 | [ ] 88886588-103700794 | [ 1 ] 74072381-88886587 | [ 3 ] 59258175-74072381 | [ 1 ] 44443968-59258174 | [ 1 ] 29629762-44443968 | [ 1 ] 14815555-29629761 |*** [ 10 ] 1349-14815555 |************************************************** [ 163 ] Storage Throughput = excellent ( 1310.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40378539 bp ( 40011188 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:08 (hh:mm:ss) Elapsed Time Round Time: 00:17:20 (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 : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2670 repeats masked totaling 946096 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10164362 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10002797 bp After Masking: 8984277 bp Masked: 10.18 % -- Input Database Coverage: 10164362 bp out of 1165749515 bp ( 0.87 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 765 HSPs Collected Number of families returned by RECON: 220 Round Time: 00:07:15 (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 : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8031 repeats masked totaling 2936642 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30214167 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30008381 bp After Masking: 26853458 bp Masked: 10.51 % -- Input Database Coverage: 40378529 bp out of 1165749515 bp ( 3.46 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:36 (hh:mm:ss) Elapsed Time, 4983 HSPs Collected Number of families returned by RECON: 1185 Round Time: 00:29:14 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25712 repeats masked totaling 9227525 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90714449 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90010106 bp After Masking: 80139610 bp Masked: 10.97 % -- Input Database Coverage: 131092978 bp out of 1165749515 bp ( 11.25 % ) Sampling Time: 00:06:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 02:30:49 (hh:mm:ss) Elapsed Time, 42608 HSPs Collected Number of families returned by RECON: 7785 Round Time: 02:38:16 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 88218 repeats masked totaling 30739000 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272076567 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 270024669 bp After Masking: 237539613 bp Masked: 12.03 % -- Input Database Coverage: 403169545 bp out of 1165749515 bp ( 34.58 % ) Sampling Time: 00:17:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23293725 Comparison Time: 18:02:13 (hh:mm:ss) Elapsed Time, 138842 HSPs Collected Number of families returned by RECON: 51353 Round Time: 18:41:41 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatScout/RECON discovery complete: 347 families found Classification Time: 00:14:20 (hh:mm:ss) Elapsed Time Program Time: 22:28:06 (hh:mm:ss) Elapsed Time