RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nhNToU/RM_11315.SunMay142148512023 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: 1684126131 Database = /dev/shm/rModeler.nhNToU/GCA_947461875.1_bHalAlb1.1 - Sequences = 188 - Bases = 1320298205 - N50 = 44572131 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 80014046-85729264 | [ 2 ] 74298828-80014045 | [ 1 ] 68583611-74298828 | [ 1 ] 62868393-68583610 | [ ] 57153176-62868393 | [ ] 51437958-57153175 | [ 1 ] 45722740-51437957 |* [ 4 ] 40007523-45722740 |* [ 6 ] 34292305-40007522 | [ 2 ] 28577088-34292305 |* [ 4 ] 22861870-28577087 |** [ 8 ] 17146652-22861869 | [ 1 ] 11431435-17146652 | [ ] 5716217-11431434 | [ 1 ] 1000-5716217 |************************************************** [ 157 ] Storage Throughput = excellent ( 1178.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030392 bp ( 40028592 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:14 (hh:mm:ss) Elapsed Time Round Time: 00:28:14 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1435 repeats masked totaling 615526 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040154 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10039554 bp After Masking: 8634610 bp Masked: 13.99 % -- Input Database Coverage: 10040154 bp out of 1320298205 bp ( 0.76 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:03 (hh:mm:ss) Elapsed Time, 13704 HSPs Collected Number of families returned by RECON: 250 Round Time: 00:08:32 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4355 repeats masked totaling 1801624 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030158 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30028958 bp After Masking: 26846690 bp Masked: 10.60 % -- Input Database Coverage: 40070312 bp out of 1320298205 bp ( 3.03 % ) Sampling Time: 00:02:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:38:47 (hh:mm:ss) Elapsed Time, 120538 HSPs Collected Number of families returned by RECON: 1514 Round Time: 00:41:34 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16398 repeats masked totaling 5772828 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026470 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90022870 bp After Masking: 79504038 bp Masked: 11.68 % -- Input Database Coverage: 130096782 bp out of 1320298205 bp ( 9.85 % ) Sampling Time: 00:09:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 04:32:58 (hh:mm:ss) Elapsed Time, 514817 HSPs Collected Number of families returned by RECON: 8322 Round Time: 04:46:45 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59382 repeats masked totaling 22136924 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032289 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 270016489 bp After Masking: 234116578 bp Masked: 13.30 % -- Input Database Coverage: 400129071 bp out of 1320298205 bp ( 30.31 % ) Sampling Time: 00:26:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 36:44:39 (hh:mm:ss) Elapsed Time, 2987704 HSPs Collected Number of families returned by RECON: 53572 Round Time: 38:08:00 (hh:mm:ss) Elapsed Time : 253 families discovered. RepeatScout/RECON discovery complete: 425 families found Classification Time: 00:39:42 (hh:mm:ss) Elapsed Time Program Time: 44:52:47 (hh:mm:ss) Elapsed Time