RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fRw92c/RM_1933084.SunMar170036442024 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: 1710661004 Database = /dev/shm/rModeler.fRw92c/GCA_036013475.1_bColLiv1.pat.W - Sequences = 870 - Bases = 1325583211 - N50 = 84824678 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198227981-212386202 | [ 1 ] 184069761-198227981 | [ ] 169911540-184069760 | [ ] 155753320-169911540 | [ 1 ] 141595099-155753319 | [ ] 127436879-141595099 | [ ] 113278658-127436878 | [ 1 ] 99120438-113278658 | [ ] 84962217-99120437 | [ ] 70803997-84962217 | [ 2 ] 56645776-70803996 | [ 1 ] 42487556-56645776 | [ ] 28329335-42487555 | [ 4 ] 14171115-28329335 | [ 9 ] 12895-14171115 |************************************************** [ 851 ] Storage Throughput = excellent ( 1455.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024580 bp ( 40023380 non ambiguous ) - Num Contigs Represented = 138 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:28 (hh:mm:ss) Elapsed Time Round Time: 00:27:22 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3116 repeats masked totaling 1161574 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008269 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10008069 bp After Masking: 8020234 bp Masked: 19.86 % -- Input Database Coverage: 10008269 bp out of 1325583211 bp ( 0.76 % ) Sampling Time: 00:12:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 476 HSPs Collected Number of families returned by RECON: 225 Round Time: 00:18:41 (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 : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8954 repeats masked totaling 3178206 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016307 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 30015307 bp After Masking: 23771240 bp Masked: 20.80 % -- Input Database Coverage: 40024576 bp out of 1325583211 bp ( 3.02 % ) Sampling Time: 00:44:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:29:15 (hh:mm:ss) Elapsed Time, 4753 HSPs Collected Number of families returned by RECON: 1121 Round Time: 01:14:06 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:10:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26257 repeats masked totaling 9289169 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013406 bp Num Contigs Represented = 242 Non ambiguous bp: Initial: 90010006 bp After Masking: 71399309 bp Masked: 20.68 % -- Input Database Coverage: 130037982 bp out of 1325583211 bp ( 9.81 % ) Sampling Time: 02:14:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 03:10:42 (hh:mm:ss) Elapsed Time, 60183 HSPs Collected Number of families returned by RECON: 6735 Round Time: 05:28:25 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 05:48:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93039 repeats masked totaling 32845530 bp(s). - TE Masking time 00:03:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034368 bp Num Contigs Represented = 447 Non ambiguous bp: Initial: 270024268 bp After Masking: 211411504 bp Masked: 21.71 % -- Input Database Coverage: 400072350 bp out of 1325583211 bp ( 30.18 % ) Sampling Time: 06:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23464675 Comparison Time: 26:08:59 (hh:mm:ss) Elapsed Time, 157418 HSPs Collected Number of families returned by RECON: 43871 Round Time: 32:34:19 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatScout/RECON discovery complete: 449 families found Classification Time: 00:31:50 (hh:mm:ss) Elapsed Time Program Time: 40:34:43 (hh:mm:ss) Elapsed Time