RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zcNpDE/RM_1224313.MonJun300838012025 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: 1751297879 Database = /dev/shm/rModeler.zcNpDE/GCF_000004195.4_UCB_Xtro_10.0 - Sequences = 167 - Bases = 1451301209 - N50 = 164033575 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202973127-217471166 | [ 1 ] 188475088-202973126 | [ ] 173977049-188475087 | [ 1 ] 159479010-173977048 | [ 1 ] 144980971-159479009 |* [ 4 ] 130482932-144980970 | [ 1 ] 115984893-130482931 | [ ] 101486854-115984892 | [ ] 86988815-101486853 | [ 1 ] 72490776-86988814 | [ ] 57992737-72490775 | [ ] 43494698-57992736 | [ 1 ] 28996659-43494697 | [ ] 14498620-28996658 | [ ] 582-14498620 |************************************************** [ 157 ] Storage Throughput = excellent ( 1128.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045528 bp ( 40002755 non ambiguous ) - Num Contigs Represented = 11 - Sequence extraction : 00:03:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:58 (hh:mm:ss) Elapsed Time Round Time: 00:35:13 (hh:mm:ss) Elapsed Time : 574 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15134 repeats masked totaling 2784961 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040056 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 10037777 bp After Masking: 6041718 bp Masked: 39.81 % -- Input Database Coverage: 10040056 bp out of 1451301209 bp ( 0.69 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:29 (hh:mm:ss) Elapsed Time, 9497 HSPs Collected Number of families returned by RECON: 1183 Round Time: 00:07:25 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49024 repeats masked totaling 8949464 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045392 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 30004898 bp After Masking: 17747782 bp Masked: 40.85 % -- Input Database Coverage: 40085448 bp out of 1451301209 bp ( 2.76 % ) Sampling Time: 00:07:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:24:00 (hh:mm:ss) Elapsed Time, 39660 HSPs Collected Number of families returned by RECON: 3923 Round Time: 00:33:03 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156322 repeats masked totaling 27983639 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90191098 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 90014201 bp After Masking: 51763939 bp Masked: 42.49 % -- Input Database Coverage: 130276546 bp out of 1451301209 bp ( 8.98 % ) Sampling Time: 00:20:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:45:10 (hh:mm:ss) Elapsed Time, 181095 HSPs Collected Number of families returned by RECON: 12673 Round Time: 03:15:01 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 527263 repeats masked totaling 94456572 bp(s). - TE Masking time 00:09:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270580148 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270029112 bp After Masking: 144396593 bp Masked: 46.53 % -- Input Database Coverage: 400856694 bp out of 1451301209 bp ( 27.62 % ) Sampling Time: 01:08:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 21:03:52 (hh:mm:ss) Elapsed Time, 599711 HSPs Collected Number of families returned by RECON: 40488 Round Time: 23:14:11 (hh:mm:ss) Elapsed Time : 969 families discovered. RepeatScout/RECON discovery complete: 2058 families found Classification Time: 01:20:58 (hh:mm:ss) Elapsed Time Program Time: 29:05:51 (hh:mm:ss) Elapsed Time