RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.nNpsxw/RM_3051031.MonApr141049592025 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: 1744652999 Database = /data/tmp/rModeler.nNpsxw/GCA_043880595.1_ASM4388059v1 - Sequences = 419 - Bases = 2124740378 - N50 = 136213956 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 227842787-244117117 | [ 1 ] 211568458-227842787 | [ ] 195294129-211568458 | [ ] 179019799-195294128 | [ 1 ] 162745470-179019799 | [ 1 ] 146471141-162745470 | [ 2 ] 130196811-146471140 | [ 1 ] 113922482-130196811 | [ 2 ] 97648153-113922482 | [ 2 ] 81373823-97648152 | [ 3 ] 65099494-81373823 | [ 1 ] 48825165-65099494 | [ 3 ] 32550835-48825164 | [ 2 ] 16276506-32550835 | [ ] 2177-16276506 |************************************************** [ 400 ] Storage Throughput = excellent ( 1511.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40991649 bp ( 40031254 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:58 (hh:mm:ss) Elapsed Time Round Time: 00:18:43 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8233 repeats masked totaling 2368851 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10252556 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10030104 bp After Masking: 7472286 bp Masked: 25.50 % -- Input Database Coverage: 10252556 bp out of 2124740378 bp ( 0.48 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:51 (hh:mm:ss) Elapsed Time, 8082 HSPs Collected Number of families returned by RECON: 823 Round Time: 00:05:07 (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 : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27182 repeats masked totaling 7267916 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30739089 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30001146 bp After Masking: 22313054 bp Masked: 25.63 % -- Input Database Coverage: 40991645 bp out of 2124740378 bp ( 1.93 % ) Sampling Time: 00:02:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:21:16 (hh:mm:ss) Elapsed Time, 22472 HSPs Collected Number of families returned by RECON: 2268 Round Time: 00:24:34 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90645 repeats masked totaling 24005837 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92582096 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 90027028 bp After Masking: 64416369 bp Masked: 28.45 % -- Input Database Coverage: 133573741 bp out of 2124740378 bp ( 6.29 % ) Sampling Time: 00:07:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2701650 Comparison Time: 02:00:41 (hh:mm:ss) Elapsed Time, 140425 HSPs Collected Number of families returned by RECON: 8345 Round Time: 02:11:06 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 326069 repeats masked totaling 80133742 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276005965 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 270039301 bp After Masking: 185158613 bp Masked: 31.43 % -- Input Database Coverage: 409579706 bp out of 2124740378 bp ( 19.28 % ) Sampling Time: 00:21:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24015915 Comparison Time: 14:12:06 (hh:mm:ss) Elapsed Time, 679206 HSPs Collected Number of families returned by RECON: 35559 Round Time: 14:46:24 (hh:mm:ss) Elapsed Time : 374 families discovered. RepeatScout/RECON discovery complete: 868 families found Classification Time: 00:23:53 (hh:mm:ss) Elapsed Time Program Time: 18:09:47 (hh:mm:ss) Elapsed Time