RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6paQwr/RM_3205486.WedDec61223072023 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: 1701894186 Database = /dev/shm/rModeler.6paQwr/GCA_963383615.1_fLipPho2.1 - Sequences = 847 - Bases = 768243328 - N50 = 32513143 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52173246-55899835 | [ 1 ] 48446657-52173246 | [ ] 44720068-48446657 | [ ] 40993479-44720068 | [ ] 37266890-40993479 | [ 2 ] 33540301-37266890 | [ 4 ] 29813712-33540301 | [ 5 ] 26087123-29813712 | [ 8 ] 22360534-26087123 | [ 1 ] 18633945-22360534 | [ 1 ] 14907356-18633945 | [ ] 11180767-14907356 | [ 1 ] 7454178-11180767 | [ ] 3727589-7454178 | [ ] 1000-3727589 |************************************************** [ 824 ] Storage Throughput = excellent ( 1417.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033182 bp ( 40026982 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:08 (hh:mm:ss) Elapsed Time Round Time: 00:22:28 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7370 repeats masked totaling 1169167 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037641 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10036841 bp After Masking: 8059418 bp Masked: 19.70 % -- Input Database Coverage: 10037641 bp out of 768243328 bp ( 1.31 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:12:28 (hh:mm:ss) Elapsed Time, 3801 HSPs Collected Number of families returned by RECON: 1019 Round Time: 00:14:30 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23376 repeats masked totaling 3682769 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035541 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 30029941 bp After Masking: 24008723 bp Masked: 20.05 % -- Input Database Coverage: 40073182 bp out of 768243328 bp ( 5.22 % ) Sampling Time: 00:05:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:39:38 (hh:mm:ss) Elapsed Time, 35213 HSPs Collected Number of families returned by RECON: 4351 Round Time: 00:46:15 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79338 repeats masked totaling 12036159 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012492 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 90000894 bp After Masking: 71216466 bp Masked: 20.87 % -- Input Database Coverage: 130085674 bp out of 768243328 bp ( 16.93 % ) Sampling Time: 00:14:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 04:07:37 (hh:mm:ss) Elapsed Time, 203395 HSPs Collected Number of families returned by RECON: 15695 Round Time: 04:31:33 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 294689 repeats masked totaling 47520964 bp(s). - TE Masking time 00:08:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050864 bp Num Contigs Represented = 419 Non ambiguous bp: Initial: 270008081 bp After Masking: 202913429 bp Masked: 24.85 % -- Input Database Coverage: 400136538 bp out of 768243328 bp ( 52.08 % ) Sampling Time: 00:50:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23829156 Comparison Time: 28:45:48 (hh:mm:ss) Elapsed Time, 588390 HSPs Collected Number of families returned by RECON: 60430 Round Time: 30:46:44 (hh:mm:ss) Elapsed Time : 996 families discovered. RepeatScout/RECON discovery complete: 1903 families found Classification Time: 01:27:13 (hh:mm:ss) Elapsed Time Program Time: 38:08:43 (hh:mm:ss) Elapsed Time