RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mJaE8T/RM_2415471.TueMar121510472024 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: 1710281446 Database = /dev/shm/rModeler.mJaE8T/GCA_035046505.1_rTilSci1.hap2 - Sequences = 350 - Bases = 1623332312 - N50 = 272452919 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 293367202-314321002 | [ 1 ] 272413403-293367202 | [ 1 ] 251459604-272413403 | [ ] 230505805-251459604 | [ 1 ] 209552006-230505805 | [ 1 ] 188598207-209552006 | [ ] 167644408-188598207 | [ ] 146690608-167644407 | [ ] 125736809-146690608 | [ 1 ] 104783010-125736809 | [ ] 83829211-104783010 | [ 1 ] 62875412-83829211 | [ 1 ] 41921613-62875412 | [ 2 ] 20967814-41921613 | [ 2 ] 14015-20967814 |************************************************** [ 339 ] Storage Throughput = excellent ( 1396.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022958 bp ( 40020758 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:34 (hh:mm:ss) Elapsed Time Round Time: 00:24:27 (hh:mm:ss) Elapsed Time : 480 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18649 repeats masked totaling 3425017 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028530 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10028130 bp After Masking: 6490983 bp Masked: 35.27 % -- Input Database Coverage: 10028530 bp out of 1623332312 bp ( 0.62 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 12387 HSPs Collected Number of families returned by RECON: 1441 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58958 repeats masked totaling 11017676 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034351 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30032551 bp After Masking: 18649635 bp Masked: 37.90 % -- Input Database Coverage: 40062881 bp out of 1623332312 bp ( 2.47 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:34:55 (hh:mm:ss) Elapsed Time, 48383 HSPs Collected Number of families returned by RECON: 4277 Round Time: 00:41:47 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 192570 repeats masked totaling 35557031 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030095 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90025895 bp After Masking: 53511596 bp Masked: 40.56 % -- Input Database Coverage: 130092976 bp out of 1623332312 bp ( 8.01 % ) Sampling Time: 00:13:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:58:42 (hh:mm:ss) Elapsed Time, 190603 HSPs Collected Number of families returned by RECON: 13569 Round Time: 03:21:29 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 642464 repeats masked totaling 118222230 bp(s). - TE Masking time 00:08:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034400 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 270021000 bp After Masking: 148756877 bp Masked: 44.91 % -- Input Database Coverage: 400127376 bp out of 1623332312 bp ( 24.65 % ) Sampling Time: 00:43:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 18:12:19 (hh:mm:ss) Elapsed Time, 528950 HSPs Collected Number of families returned by RECON: 45740 Round Time: 19:54:55 (hh:mm:ss) Elapsed Time : 1040 families discovered. RepeatScout/RECON discovery complete: 2073 families found Classification Time: 01:10:55 (hh:mm:ss) Elapsed Time Program Time: 25:41:22 (hh:mm:ss) Elapsed Time