RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TqLNVe/RM_1223637.SunMar311125422024 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: 1711909542 Database = /dev/shm/rModeler.TqLNVe/GCA_963932225.1_bLarFus1.1 - Sequences = 1367 - Bases = 1324286540 - N50 = 94813656 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203909867-218474787 | [ 1 ] 189344948-203909867 | [ ] 174780029-189344948 | [ ] 160215110-174780029 | [ 1 ] 145650191-160215110 | [ ] 131085272-145650191 | [ ] 116520353-131085272 | [ 1 ] 101955433-116520352 | [ ] 87390514-101955433 | [ 1 ] 72825595-87390514 | [ 3 ] 58260676-72825595 | [ ] 43695757-58260676 | [ 3 ] 29130838-43695757 | [ ] 14565919-29130838 | [ 5 ] 1000-14565919 |************************************************** [ 1352 ] Storage Throughput = excellent ( 1006.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015074 bp ( 40011707 non ambiguous ) - Num Contigs Represented = 124 - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:22 (hh:mm:ss) Elapsed Time Round Time: 00:24:03 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1504 repeats masked totaling 609906 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030948 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10030148 bp After Masking: 8747921 bp Masked: 12.78 % -- Input Database Coverage: 10030948 bp out of 1324286540 bp ( 0.76 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:20:08 (hh:mm:ss) Elapsed Time, 23751 HSPs Collected Number of families returned by RECON: 241 Round Time: 00:21:18 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5715 repeats masked totaling 2075070 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027056 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30024489 bp After Masking: 26426567 bp Masked: 11.98 % -- Input Database Coverage: 40058004 bp out of 1324286540 bp ( 3.02 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 01:21:49 (hh:mm:ss) Elapsed Time, 257179 HSPs Collected Number of families returned by RECON: 1294 Round Time: 01:26:54 (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 : 00:04:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15160 repeats masked totaling 5773991 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039543 bp Num Contigs Represented = 236 Non ambiguous bp: Initial: 90033421 bp After Masking: 79085139 bp Masked: 12.16 % -- Input Database Coverage: 130097547 bp out of 1324286540 bp ( 9.82 % ) Sampling Time: 00:10:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 07:00:40 (hh:mm:ss) Elapsed Time, 1908542 HSPs Collected Number of families returned by RECON: 7315 Round Time: 07:13:25 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55789 repeats masked totaling 19711842 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032105 bp Num Contigs Represented = 602 Non ambiguous bp: Initial: 270010890 bp After Masking: 234194298 bp Masked: 13.26 % -- Input Database Coverage: 400129652 bp out of 1324286540 bp ( 30.21 % ) Sampling Time: 00:30:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23870595 Comparison Time: 67:30:17 (hh:mm:ss) Elapsed Time, 34415585 HSPs Collected Number of families returned by RECON: 45252 Round Time: 68:38:11 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:23:00 (hh:mm:ss) Elapsed Time Program Time: 78:26:51 (hh:mm:ss) Elapsed Time