RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.KGIKfT/RM_2890164.TueApr150718572025 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: 1744726736 Database = /data/tmp/rModeler.KGIKfT/GCA_043728065.1_ASM4372806v1 - Sequences = 2194 - Bases = 2302456897 - N50 = 93837039 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 112947005-121013437 | [ 1 ] 104880573-112947004 | [ 4 ] 96814142-104880573 | [ 3 ] 88747710-96814141 | [ 3 ] 80681278-88747709 | [ 1 ] 72614847-80681278 | [ 1 ] 64548415-72614846 | [ 2 ] 56481983-64548414 | [ 4 ] 48415552-56481983 | [ 1 ] 40349120-48415551 | [ 4 ] 32282688-40349119 | [ ] 24216257-32282688 | [ 5 ] 16149825-24216256 | [ 2 ] 8083393-16149824 | [ 1 ] 16962-8083393 |************************************************** [ 2162 ] Storage Throughput = excellent ( 1836.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005542 bp ( 40005542 non ambiguous ) - Num Contigs Represented = 144 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:11 (hh:mm:ss) Elapsed Time Round Time: 00:15:06 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6594 repeats masked totaling 1755780 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034752 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10034752 bp After Masking: 7181817 bp Masked: 28.43 % -- Input Database Coverage: 10034752 bp out of 2302456897 bp ( 0.44 % ) Sampling Time: 00:09:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:11 (hh:mm:ss) Elapsed Time, 7543 HSPs Collected Number of families returned by RECON: 822 Round Time: 00:13:28 (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 : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22659 repeats masked totaling 5882829 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010845 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 30010845 bp After Masking: 21312509 bp Masked: 28.98 % -- Input Database Coverage: 40045597 bp out of 2302456897 bp ( 1.74 % ) Sampling Time: 00:28:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:21:41 (hh:mm:ss) Elapsed Time, 65623 HSPs Collected Number of families returned by RECON: 2567 Round Time: 00:50:56 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79928 repeats masked totaling 20747879 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028276 bp Num Contigs Represented = 225 Non ambiguous bp: Initial: 90028276 bp After Masking: 61913396 bp Masked: 31.23 % -- Input Database Coverage: 130073873 bp out of 2302456897 bp ( 5.65 % ) Sampling Time: 01:02:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 02:00:18 (hh:mm:ss) Elapsed Time, 348624 HSPs Collected Number of families returned by RECON: 9548 Round Time: 03:05:02 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:27:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 283305 repeats masked totaling 71456247 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012099 bp Num Contigs Represented = 562 Non ambiguous bp: Initial: 270009297 bp After Masking: 177714419 bp Masked: 34.18 % -- Input Database Coverage: 400085972 bp out of 2302456897 bp ( 17.38 % ) Sampling Time: 03:35:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23691286 Comparison Time: 13:30:31 (hh:mm:ss) Elapsed Time, 2102022 HSPs Collected Number of families returned by RECON: 37874 Round Time: 17:17:59 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatScout/RECON discovery complete: 782 families found Classification Time: 00:18:41 (hh:mm:ss) Elapsed Time Program Time: 22:01:12 (hh:mm:ss) Elapsed Time