RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.x6yfXr/RM_623961.SunDec81308272024 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: 1733692106 Database = /scratch/tmp/rModeler.x6yfXr/GCA_044704955.1_sPriJap1.hap1 - Sequences = 4317 - Bases = 5923050865 - N50 = 229984596 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 509820876-546236482 | [ 1 ] 473405271-509820876 | [ ] 436989665-473405270 | [ ] 400574060-436989665 | [ ] 364158455-400574060 | [ 1 ] 327742849-364158454 | [ 1 ] 291327244-327742849 | [ 2 ] 254911638-291327243 | [ 1 ] 218496033-254911638 | [ 5 ] 182080428-218496033 | [ 4 ] 145664822-182080427 | [ ] 109249217-145664822 | [ 3 ] 72833611-109249216 | [ 3 ] 36418006-72833611 | [ 5 ] 2401-36418006 |************************************************** [ 4291 ] Storage Throughput = excellent ( 1592.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009563 bp ( 40001363 non ambiguous ) - Num Contigs Represented = 163 - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:43 (hh:mm:ss) Elapsed Time Round Time: 00:16:31 (hh:mm:ss) Elapsed Time : 577 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15536 repeats masked totaling 6035620 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023436 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 10021236 bp After Masking: 2443563 bp Masked: 75.62 % -- Input Database Coverage: 10023436 bp out of 5923050865 bp ( 0.17 % ) Sampling Time: 00:05:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:38 (hh:mm:ss) Elapsed Time, 3598 HSPs Collected Number of families returned by RECON: 635 Round Time: 00:08:15 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47893 repeats masked totaling 18108121 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026125 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 30020125 bp After Masking: 6746191 bp Masked: 77.53 % -- Input Database Coverage: 40049561 bp out of 5923050865 bp ( 0.68 % ) Sampling Time: 00:16:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:09:09 (hh:mm:ss) Elapsed Time, 19269 HSPs Collected Number of families returned by RECON: 1898 Round Time: 00:25:31 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143506 repeats masked totaling 53542459 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027680 bp Num Contigs Represented = 247 Non ambiguous bp: Initial: 90008752 bp After Masking: 20064788 bp Masked: 77.71 % -- Input Database Coverage: 130077241 bp out of 5923050865 bp ( 2.20 % ) Sampling Time: 00:42:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 00:40:00 (hh:mm:ss) Elapsed Time, 138214 HSPs Collected Number of families returned by RECON: 5578 Round Time: 01:25:48 (hh:mm:ss) Elapsed Time : 260 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:52:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 477669 repeats masked totaling 171794580 bp(s). - TE Masking time 00:03:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270082612 bp Num Contigs Represented = 622 Non ambiguous bp: Initial: 270029662 bp After Masking: 52256313 bp Masked: 80.65 % -- Input Database Coverage: 400159853 bp out of 5923050865 bp ( 6.76 % ) Sampling Time: 02:10:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23533230 Comparison Time: 03:21:37 (hh:mm:ss) Elapsed Time, 402937 HSPs Collected Number of families returned by RECON: 14553 Round Time: 05:40:58 (hh:mm:ss) Elapsed Time : 635 families discovered. RepeatScout/RECON discovery complete: 1531 families found Classification Time: 00:29:03 (hh:mm:ss) Elapsed Time Program Time: 08:26:06 (hh:mm:ss) Elapsed Time