RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.h7MLby/RM_312169.SatFeb222259512025 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: 1740293989 Database = /data/tmp/rModeler.h7MLby/GCA_964417175.1_bLarArg3.hap1.1 - Sequences = 401 - Bases = 1417856064 - N50 = 99453021 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206088281-220808802 | [ 1 ] 191367761-206088281 | [ ] 176647241-191367761 | [ ] 161926721-176647241 | [ 1 ] 147206201-161926721 | [ ] 132485681-147206201 | [ ] 117765161-132485681 | [ 1 ] 103044640-117765160 | [ ] 88324120-103044640 | [ 2 ] 73603600-88324120 | [ 2 ] 58883080-73603600 | [ 1 ] 44162560-58883080 | [ 2 ] 29442040-44162560 | [ 1 ] 14721520-29442040 | [ 5 ] 1000-14721520 |************************************************** [ 385 ] Storage Throughput = excellent ( 1152.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019220 bp ( 40017820 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:34 (hh:mm:ss) Elapsed Time Round Time: 00:28:12 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2374 repeats masked totaling 887967 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027944 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10027544 bp After Masking: 8622665 bp Masked: 14.01 % -- Input Database Coverage: 10027944 bp out of 1417856064 bp ( 0.71 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:34:12 (hh:mm:ss) Elapsed Time, 83136 HSPs Collected Number of families returned by RECON: 247 Round Time: 00:35:07 (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 : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6188 repeats masked totaling 2585249 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031276 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 30030276 bp After Masking: 25647384 bp Masked: 14.59 % -- Input Database Coverage: 40059220 bp out of 1417856064 bp ( 2.83 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 01:43:39 (hh:mm:ss) Elapsed Time, 729731 HSPs Collected Number of families returned by RECON: 1191 Round Time: 01:47:20 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19591 repeats masked totaling 7772694 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017228 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 90009628 bp After Masking: 76263516 bp Masked: 15.27 % -- Input Database Coverage: 130076448 bp out of 1417856064 bp ( 9.17 % ) Sampling Time: 00:08:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 10:52:28 (hh:mm:ss) Elapsed Time, 8081334 HSPs Collected Number of families returned by RECON: 6680 Round Time: 11:04:29 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69892 repeats masked totaling 26037007 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036463 bp Num Contigs Represented = 231 Non ambiguous bp: Initial: 270015030 bp After Masking: 226934599 bp Masked: 15.95 % -- Input Database Coverage: 400112911 bp out of 1417856064 bp ( 28.22 % ) Sampling Time: 00:19:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 70:16:00 (hh:mm:ss) Elapsed Time, 67531052 HSPs Collected Number of families returned by RECON: 41545 Round Time: 71:12:50 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatScout/RECON discovery complete: 391 families found Classification Time: 00:15:54 (hh:mm:ss) Elapsed Time Program Time: 85:23:52 (hh:mm:ss) Elapsed Time