RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mv3r8B/RM_14662.FriJul192041392024 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: 1721446893 Database = /dev/shm/rModeler.mv3r8B/GCF_016077235.1_ASM1607723v1 - Sequences = 2003 - Bases = 1086882241 - N50 = 1363955 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 7583050-8124452 | [ 1 ] 7041649-7583050 | [ ] 6500247-7041648 | [ ] 5958846-6500247 | [ 1 ] 5417444-5958845 | [ 1 ] 4876043-5417444 | [ 5 ] 4334641-4876042 | [ 10 ] 3793240-4334641 | [ 8 ] 3251838-3793239 | [ 11 ] 2710437-3251838 | [ 13 ] 2169035-2710436 |* [ 43 ] 1627634-2169035 |** [ 73 ] 1086232-1627633 |***** [ 154 ] 544831-1086232 |********* [ 279 ] 3430-544831 |************************************************** [ 1404 ] Storage Throughput = good ( 767.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034472 bp ( 40034472 non ambiguous ) - Num Contigs Represented = 606 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:07 (hh:mm:ss) Elapsed Time Round Time: 00:33:04 (hh:mm:ss) Elapsed Time : 751 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12602 repeats masked totaling 3213059 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009119 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 10009119 bp After Masking: 6541618 bp Masked: 34.64 % -- Input Database Coverage: 10009119 bp out of 1086882241 bp ( 0.92 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:24:05 (hh:mm:ss) Elapsed Time, 5330 HSPs Collected Number of families returned by RECON: 1158 Round Time: 00:25:53 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38791 repeats masked totaling 9564410 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025302 bp Num Contigs Represented = 496 Non ambiguous bp: Initial: 30025302 bp After Masking: 19552091 bp Masked: 34.88 % -- Input Database Coverage: 40034421 bp out of 1086882241 bp ( 3.68 % ) Sampling Time: 00:03:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 302253 Comparison Time: 01:17:43 (hh:mm:ss) Elapsed Time, 39068 HSPs Collected Number of families returned by RECON: 3916 Round Time: 01:23:57 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125658 repeats masked totaling 30254798 bp(s). - TE Masking time 00:03:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031283 bp Num Contigs Represented = 942 Non ambiguous bp: Initial: 90031283 bp After Masking: 56751225 bp Masked: 36.96 % -- Input Database Coverage: 130065704 bp out of 1086882241 bp ( 11.97 % ) Sampling Time: 00:11:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2715615 Comparison Time: 05:48:06 (hh:mm:ss) Elapsed Time, 212431 HSPs Collected Number of families returned by RECON: 11342 Round Time: 06:13:35 (hh:mm:ss) Elapsed Time : 468 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438023 repeats masked totaling 105620766 bp(s). - TE Masking time 00:15:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270006965 bp Num Contigs Represented = 1402 Non ambiguous bp: Initial: 270006965 bp After Masking: 156059519 bp Masked: 42.20 % -- Input Database Coverage: 400072669 bp out of 1086882241 bp ( 36.81 % ) Sampling Time: 00:39:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24580566 Comparison Time: 30:04:06 (hh:mm:ss) Elapsed Time, 545659 HSPs Collected Number of families returned by RECON: 37771 Round Time: 31:45:26 (hh:mm:ss) Elapsed Time : 1002 families discovered. RepeatScout/RECON discovery complete: 2335 families found Classification Time: 01:50:53 (hh:mm:ss) Elapsed Time Program Time: 42:12:48 (hh:mm:ss) Elapsed Time