RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.syaOmW/RM_933285.WedNov130636482024 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: 1731508608 Database = /scratch/tmp/rModeler.syaOmW/GCA_040894355.1_rMyuGeo1.pri.20230808 - Sequences = 129 - Bases = 1980051792 - N50 = 146335920 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 290689360-311452600 | [ 1 ] 269926120-290689360 | [ ] 249162880-269926120 | [ ] 228399640-249162880 | [ 1 ] 207636400-228399640 | [ ] 186873160-207636400 | [ 1 ] 166109920-186873160 | [ ] 145346680-166109920 | [ 1 ] 124583440-145346680 | [ ] 103820200-124583440 |* [ 4 ] 83056960-103820200 | [ 2 ] 62293720-83056960 | [ 1 ] 41530480-62293720 | [ 2 ] 20767240-41530480 |** [ 5 ] 4000-20767240 |************************************************* [ 111 ] Storage Throughput = excellent ( 1431.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015728 bp ( 40015328 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:59 (hh:mm:ss) Elapsed Time Round Time: 00:10:49 (hh:mm:ss) Elapsed Time : 476 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 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11441 repeats masked totaling 2089128 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005348 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10005348 bp After Masking: 7718851 bp Masked: 22.85 % -- Input Database Coverage: 10005348 bp out of 1980051792 bp ( 0.51 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 18962 HSPs Collected Number of families returned by RECON: 1711 Round Time: 00:04:06 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40255 repeats masked totaling 7358953 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010376 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30009976 bp After Masking: 22425725 bp Masked: 25.27 % -- Input Database Coverage: 40015724 bp out of 1980051792 bp ( 2.02 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:02 (hh:mm:ss) Elapsed Time, 65756 HSPs Collected Number of families returned by RECON: 5592 Round Time: 00:15:53 (hh:mm:ss) Elapsed Time : 154 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139192 repeats masked totaling 26610400 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005852 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90005452 bp After Masking: 62004858 bp Masked: 31.11 % -- Input Database Coverage: 130021576 bp out of 1980051792 bp ( 6.57 % ) Sampling Time: 00:06:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:14:48 (hh:mm:ss) Elapsed Time, 246981 HSPs Collected Number of families returned by RECON: 15085 Round Time: 01:26:50 (hh:mm:ss) Elapsed Time : 468 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482008 repeats masked totaling 95848656 bp(s). - TE Masking time 00:03:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017802 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 270016202 bp After Masking: 170384890 bp Masked: 36.90 % -- Input Database Coverage: 400039378 bp out of 1980051792 bp ( 20.20 % ) Sampling Time: 00:20:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 08:18:38 (hh:mm:ss) Elapsed Time, 610660 HSPs Collected Number of families returned by RECON: 48638 Round Time: 09:10:34 (hh:mm:ss) Elapsed Time : 1045 families discovered. RepeatScout/RECON discovery complete: 2177 families found Classification Time: 00:44:03 (hh:mm:ss) Elapsed Time Program Time: 11:52:15 (hh:mm:ss) Elapsed Time