RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.IaO3or/RM_800386.SatApr121652452025 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: 1744501965 Database = /data/tmp/rModeler.IaO3or/GCA_046562895.1_mTriInu1_haplotype_2 - Sequences = 401 - Bases = 3320339069 - N50 = 137272433 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215867889-231286350 | [ 1 ] 200449429-215867889 | [ 2 ] 185030969-200449429 | [ 2 ] 169612509-185030969 | [ 1 ] 154194049-169612509 | [ ] 138775588-154194048 | [ 2 ] 123357128-138775588 | [ 2 ] 107938668-123357128 | [ 3 ] 92520208-107938668 | [ 1 ] 77101748-92520208 | [ 6 ] 61683287-77101747 | [ 5 ] 46264827-61683287 | [ 2 ] 30846367-46264827 | [ 1 ] 15427907-30846367 | [ 1 ] 9447-15427907 |************************************************** [ 372 ] Storage Throughput = excellent ( 1549.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022608 bp ( 40022408 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:36 (hh:mm:ss) Elapsed Time Round Time: 00:22:36 (hh:mm:ss) Elapsed Time : 253 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15552 repeats masked totaling 4714850 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010357 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10010357 bp After Masking: 5240923 bp Masked: 47.64 % -- Input Database Coverage: 10010357 bp out of 3320339069 bp ( 0.30 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 5755 HSPs Collected Number of families returned by RECON: 707 Round Time: 00:04:13 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49827 repeats masked totaling 14796484 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012171 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30011971 bp After Masking: 15077367 bp Masked: 49.76 % -- Input Database Coverage: 40022528 bp out of 3320339069 bp ( 1.21 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:36 (hh:mm:ss) Elapsed Time, 17518 HSPs Collected Number of families returned by RECON: 1895 Round Time: 00:16:05 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154367 repeats masked totaling 46592195 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010414 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90009414 bp After Masking: 42947314 bp Masked: 52.29 % -- Input Database Coverage: 130032942 bp out of 3320339069 bp ( 3.92 % ) Sampling Time: 00:06:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:14:54 (hh:mm:ss) Elapsed Time, 70526 HSPs Collected Number of families returned by RECON: 6461 Round Time: 01:22:40 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 488219 repeats masked totaling 145191716 bp(s). - TE Masking time 00:03:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027843 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 270023643 bp After Masking: 123461388 bp Masked: 54.28 % -- Input Database Coverage: 400060785 bp out of 3320339069 bp ( 12.05 % ) Sampling Time: 00:19:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 08:35:45 (hh:mm:ss) Elapsed Time, 208547 HSPs Collected Number of families returned by RECON: 24991 Round Time: 09:05:42 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 834 families found Classification Time: 00:24:34 (hh:mm:ss) Elapsed Time Program Time: 11:35:50 (hh:mm:ss) Elapsed Time