RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0UOJMK/RM_340446.FriJul50705522024 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: 1720188351 Database = /dev/shm/rModeler.0UOJMK/GCF_034702125.1_IST_EnEncr_1.0 - Sequences = 1922 - Bases = 1435200347 - N50 = 56824834 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 56251462-60269354 | [ 13 ] 52233570-56251461 | [ 7 ] 48215678-52233569 | [ 4 ] 44197787-48215678 | [ ] 40179895-44197786 | [ ] 36162003-40179894 | [ ] 32144111-36162002 | [ ] 28126220-32144111 | [ ] 24108328-28126219 | [ ] 20090436-24108327 | [ ] 16072544-20090435 | [ ] 12054653-16072544 | [ ] 8036761-12054652 | [ ] 4018869-8036760 | [ ] 978-4018869 |************************************************** [ 1898 ] Storage Throughput = excellent ( 1348.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025283 bp ( 40020521 non ambiguous ) - Num Contigs Represented = 110 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:56 (hh:mm:ss) Elapsed Time Round Time: 00:29:17 (hh:mm:ss) Elapsed Time : 1019 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16306 repeats masked totaling 2964725 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022643 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10021397 bp After Masking: 5779402 bp Masked: 42.33 % -- Input Database Coverage: 10022643 bp out of 1435200347 bp ( 0.70 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:05:38 (hh:mm:ss) Elapsed Time, 5614 HSPs Collected Number of families returned by RECON: 1167 Round Time: 00:08:55 (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 : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47847 repeats masked totaling 8573509 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042543 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30039025 bp After Masking: 17622495 bp Masked: 41.33 % -- Input Database Coverage: 40065186 bp out of 1435200347 bp ( 2.79 % ) Sampling Time: 00:09:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 00:27:01 (hh:mm:ss) Elapsed Time, 36508 HSPs Collected Number of families returned by RECON: 3990 Round Time: 00:37:00 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148777 repeats masked totaling 26272254 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042482 bp Num Contigs Represented = 216 Non ambiguous bp: Initial: 90025908 bp After Masking: 51859972 bp Masked: 42.39 % -- Input Database Coverage: 130107668 bp out of 1435200347 bp ( 9.07 % ) Sampling Time: 00:26:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2694681 Comparison Time: 02:03:03 (hh:mm:ss) Elapsed Time, 294605 HSPs Collected Number of families returned by RECON: 12574 Round Time: 02:36:41 (hh:mm:ss) Elapsed Time : 561 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:09:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 514735 repeats masked totaling 95067681 bp(s). - TE Masking time 00:11:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270068140 bp Num Contigs Represented = 476 Non ambiguous bp: Initial: 270025618 bp After Masking: 139933798 bp Masked: 48.18 % -- Input Database Coverage: 400175808 bp out of 1435200347 bp ( 27.88 % ) Sampling Time: 01:27:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24210361 Comparison Time: 20:20:56 (hh:mm:ss) Elapsed Time, 783074 HSPs Collected Number of families returned by RECON: 40703 Round Time: 22:25:40 (hh:mm:ss) Elapsed Time : 1223 families discovered. RepeatScout/RECON discovery complete: 2876 families found Classification Time: 01:27:53 (hh:mm:ss) Elapsed Time Program Time: 27:45:26 (hh:mm:ss) Elapsed Time