RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5fyxkY/RM_299715.SunJan291703582023 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: 1675040636 Database = /dev/shm/rModeler.5fyxkY/GCF_900747795.2_fErpCal1.3 - Sequences = 169 - Bases = 3613551144 - N50 = 252032905 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 332991257-356776219 | [ 3 ] 309206295-332991256 | [ 1 ] 285421334-309206295 | [ ] 261636372-285421333 | [ ] 237851411-261636372 | [ 1 ] 214066449-237851410 | [ 1 ] 190281488-214066449 | [ 3 ] 166496526-190281487 | [ 2 ] 142711565-166496526 | [ 2 ] 118926603-142711564 | [ ] 95141642-118926603 |* [ 4 ] 71356680-95141641 | [ 1 ] 47571719-71356680 | [ ] 23786757-47571718 | [ ] 1796-23786757 |************************************************** [ 151 ] Storage Throughput = excellent ( 1367.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40314528 bp ( 40012282 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:15 (hh:mm:ss) Elapsed Time Round Time: 00:21:42 (hh:mm:ss) Elapsed Time : 828 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16491 repeats masked totaling 4504973 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080195 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10021859 bp After Masking: 5329853 bp Masked: 46.82 % -- Input Database Coverage: 10080195 bp out of 3613551144 bp ( 0.28 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:37 (hh:mm:ss) Elapsed Time, 8141 HSPs Collected Number of families returned by RECON: 1520 Round Time: 00:10:43 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52451 repeats masked totaling 13983458 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30274258 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30030348 bp After Masking: 15473243 bp Masked: 48.47 % -- Input Database Coverage: 40354453 bp out of 3613551144 bp ( 1.12 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:39:50 (hh:mm:ss) Elapsed Time, 57119 HSPs Collected Number of families returned by RECON: 4599 Round Time: 00:46:01 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 165839 repeats masked totaling 44466327 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91075196 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90019439 bp After Masking: 43824098 bp Masked: 51.32 % -- Input Database Coverage: 131429649 bp out of 3613551144 bp ( 3.64 % ) Sampling Time: 00:15:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 03:22:45 (hh:mm:ss) Elapsed Time, 257094 HSPs Collected Number of families returned by RECON: 12589 Round Time: 03:45:40 (hh:mm:ss) Elapsed Time : 563 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 584023 repeats masked totaling 150672031 bp(s). - TE Masking time 00:06:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271928023 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 270013638 bp After Masking: 114043147 bp Masked: 57.76 % -- Input Database Coverage: 403357672 bp out of 3613551144 bp ( 11.16 % ) Sampling Time: 00:45:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 15:19:59 (hh:mm:ss) Elapsed Time, 684869 HSPs Collected Number of families returned by RECON: 32057 Round Time: 16:38:54 (hh:mm:ss) Elapsed Time : 1245 families discovered. RepeatScout/RECON discovery complete: 2791 families found Classification Time: 01:22:43 (hh:mm:ss) Elapsed Time Program Time: 23:05:43 (hh:mm:ss) Elapsed Time