RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SfUndL/RM_683806.MonJul281600062025 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: 1753743603 Database = /dev/shm/rModeler.SfUndL/GCA_040438655.1_ASM4043865v1 - Sequences = 268216 - Bases = 11554056998 - N50 = 37402 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32060782-34350599 | [ 1 ] 29770965-32060781 | [ ] 27481148-29770964 | [ ] 25191331-27481147 | [ ] 22901514-25191330 | [ ] 20611697-22901513 | [ 1 ] 18321880-20611696 | [ ] 16032064-18321880 | [ 1 ] 13742247-16032063 | [ 4 ] 11452430-13742246 | [ 5 ] 9162613-11452429 | [ 6 ] 6872796-9162612 | [ 15 ] 4582979-6872795 | [ 51 ] 2293162-4582978 | [ 242 ] 3346-2293162 |************************************************** [ 267890 ] Storage Throughput = excellent ( 1146.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037029 bp ( 40037029 non ambiguous ) - Num Contigs Represented = 1264 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:30:32 (hh:mm:ss) Elapsed Time Round Time: 01:02:21 (hh:mm:ss) Elapsed Time : 649 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10865 repeats masked totaling 5568448 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024402 bp Num Contigs Represented = 329 Non ambiguous bp: Initial: 10024402 bp After Masking: 2232487 bp Masked: 77.73 % -- Input Database Coverage: 10024402 bp out of 11554056998 bp ( 0.09 % ) Sampling Time: 00:15:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 55945 Comparison Time: 00:04:15 (hh:mm:ss) Elapsed Time, 2652 HSPs Collected Number of families returned by RECON: 640 Round Time: 00:19:45 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32158 repeats masked totaling 16998793 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012552 bp Num Contigs Represented = 951 Non ambiguous bp: Initial: 30012552 bp After Masking: 6679281 bp Masked: 77.75 % -- Input Database Coverage: 40036954 bp out of 11554056998 bp ( 0.35 % ) Sampling Time: 00:24:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 481671 Comparison Time: 00:16:23 (hh:mm:ss) Elapsed Time, 27735 HSPs Collected Number of families returned by RECON: 2109 Round Time: 00:42:07 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:15:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 103533 repeats masked totaling 52590319 bp(s). - TE Masking time 00:03:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008880 bp Num Contigs Represented = 2909 Non ambiguous bp: Initial: 90008880 bp After Masking: 20284639 bp Masked: 77.46 % -- Input Database Coverage: 130045834 bp out of 11554056998 bp ( 1.13 % ) Sampling Time: 01:19:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4713985 Comparison Time: 01:22:28 (hh:mm:ss) Elapsed Time, 175669 HSPs Collected Number of families returned by RECON: 6067 Round Time: 03:11:03 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:24:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 339248 repeats masked totaling 169132038 bp(s). - TE Masking time 00:14:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004651 bp Num Contigs Represented = 8341 Non ambiguous bp: Initial: 270004651 bp After Masking: 48515650 bp Masked: 82.03 % -- Input Database Coverage: 400050485 bp out of 11554056998 bp ( 3.46 % ) Sampling Time: 03:40:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42012361 Comparison Time: 07:55:14 (hh:mm:ss) Elapsed Time, 533596 HSPs Collected Number of families returned by RECON: 16328 Round Time: 12:00:17 (hh:mm:ss) Elapsed Time : 658 families discovered. RepeatScout/RECON discovery complete: 1644 families found Classification Time: 01:31:41 (hh:mm:ss) Elapsed Time Program Time: 18:47:14 (hh:mm:ss) Elapsed Time