RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6Jeyhq/RM_5422.ThuNov302250032023 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: 1701413402 Database = /dev/shm/rModeler.6Jeyhq/GCA_030015355.1_fTriRos1.hap2 - Sequences = 302 - Bases = 996754446 - N50 = 38093692 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 76866593-82356993 | [ 1 ] 71376193-76866592 | [ ] 65885794-71376193 | [ ] 60395394-65885793 | [ 1 ] 54904995-60395394 | [ 1 ] 49414595-54904994 | [ 1 ] 43924196-49414595 | [ 1 ] 38433796-43924195 | [ 4 ] 32943397-38433796 | [ 3 ] 27452997-32943396 |* [ 6 ] 21962598-27452997 | [ 2 ] 16472198-21962597 |* [ 6 ] 10981799-16472198 | [ 2 ] 5491399-10981798 | [ 1 ] 1000-5491399 |************************************************** [ 273 ] Storage Throughput = excellent ( 1130.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011899 bp ( 40010299 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:55 (hh:mm:ss) Elapsed Time Round Time: 00:31:53 (hh:mm:ss) Elapsed Time : 707 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20259 repeats masked totaling 4218201 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033416 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10032616 bp After Masking: 5047646 bp Masked: 49.69 % -- Input Database Coverage: 10033416 bp out of 996754446 bp ( 1.01 % ) Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 4437 HSPs Collected Number of families returned by RECON: 1056 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61028 repeats masked totaling 12752441 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018491 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30017691 bp After Masking: 15343583 bp Masked: 48.88 % -- Input Database Coverage: 40051907 bp out of 996754446 bp ( 4.02 % ) Sampling Time: 00:06:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:24:32 (hh:mm:ss) Elapsed Time, 42020 HSPs Collected Number of families returned by RECON: 3831 Round Time: 00:32:42 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191471 repeats masked totaling 38924131 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015890 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90011890 bp After Masking: 45068157 bp Masked: 49.93 % -- Input Database Coverage: 130067797 bp out of 996754446 bp ( 13.05 % ) Sampling Time: 00:19:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:39:55 (hh:mm:ss) Elapsed Time, 195165 HSPs Collected Number of families returned by RECON: 11974 Round Time: 03:08:48 (hh:mm:ss) Elapsed Time : 370 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 638453 repeats masked totaling 127452315 bp(s). - TE Masking time 00:12:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033553 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 270023753 bp After Masking: 124096054 bp Masked: 54.04 % -- Input Database Coverage: 400101350 bp out of 996754446 bp ( 40.14 % ) Sampling Time: 01:06:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 20:33:50 (hh:mm:ss) Elapsed Time, 506302 HSPs Collected Number of families returned by RECON: 38436 Round Time: 22:39:35 (hh:mm:ss) Elapsed Time : 891 families discovered. RepeatScout/RECON discovery complete: 2064 families found Classification Time: 01:33:43 (hh:mm:ss) Elapsed Time Program Time: 28:34:31 (hh:mm:ss) Elapsed Time