RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ztW1iD/RM_8828.WedJan40659072023 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: 1672844346 Database = /dev/shm/rModeler.ztW1iD/GCA_003957555.2_bCalAnn1_v1.p - Sequences = 160 - Bases = 1059706240 - N50 = 114810999 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184381261-197551010 | [ 1 ] 171211512-184381260 | [ ] 158041763-171211511 | [ ] 144872014-158041762 | [ 1 ] 131702265-144872013 | [ ] 118532516-131702264 | [ ] 105362767-118532515 | [ 1 ] 92193019-105362767 | [ ] 79023270-92193018 | [ ] 65853521-79023269 | [ 1 ] 52683772-65853520 | [ ] 39514023-52683771 | [ 2 ] 26344274-39514022 |* [ 4 ] 13174525-26344273 |*** [ 11 ] 4777-13174525 |************************************************** [ 139 ] Storage Throughput = excellent ( 1098.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40600379 bp ( 40033002 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:35 (hh:mm:ss) Elapsed Time Round Time: 00:27:24 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3325 repeats masked totaling 990873 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10201750 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10038829 bp After Masking: 8980093 bp Masked: 10.55 % -- Input Database Coverage: 10201750 bp out of 1059706240 bp ( 0.96 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:07:35 (hh:mm:ss) Elapsed Time, 700 HSPs Collected Number of families returned by RECON: 284 Round Time: 00:08:39 (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 : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9373 repeats masked totaling 2695599 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30438529 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30034073 bp After Masking: 27090752 bp Masked: 9.80 % -- Input Database Coverage: 40640279 bp out of 1059706240 bp ( 3.84 % ) Sampling Time: 00:02:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:43:22 (hh:mm:ss) Elapsed Time, 4552 HSPs Collected Number of families returned by RECON: 1768 Round Time: 00:46:42 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28981 repeats masked totaling 8181735 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91268592 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90027005 bp After Masking: 80975418 bp Masked: 10.05 % -- Input Database Coverage: 131908871 bp out of 1059706240 bp ( 12.45 % ) Sampling Time: 00:08:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 05:18:13 (hh:mm:ss) Elapsed Time, 42491 HSPs Collected Number of families returned by RECON: 11698 Round Time: 05:29:47 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90979 repeats masked totaling 24443542 bp(s). - TE Masking time 00:03:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274580108 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 270008463 bp After Masking: 243240336 bp Masked: 9.91 % -- Input Database Coverage: 406488979 bp out of 1059706240 bp ( 38.36 % ) Sampling Time: 00:25:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23643126 Comparison Time: 44:24:18 (hh:mm:ss) Elapsed Time, 197162 HSPs Collected Number of families returned by RECON: 80943 Round Time: 46:19:41 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatScout/RECON discovery complete: 366 families found Classification Time: 00:23:38 (hh:mm:ss) Elapsed Time Program Time: 53:35:51 (hh:mm:ss) Elapsed Time