RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BqJlDB/RM_3416841.FriMar151420312024 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: 1710537630 Database = /dev/shm/rModeler.BqJlDB/GCA_036010775.1_bColLiv1.mat - Sequences = 650 - Bases = 1181506259 - N50 = 121985148 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198565191-212747336 | [ 1 ] 184383047-198565191 | [ ] 170200903-184383047 | [ ] 156018758-170200902 | [ 1 ] 141836614-156018758 | [ ] 127654470-141836614 | [ ] 113472326-127654470 | [ 1 ] 99290181-113472325 | [ ] 85108037-99290181 | [ ] 70925893-85108037 | [ 1 ] 56743749-70925893 | [ 1 ] 42561604-56743748 | [ ] 28379460-42561604 | [ 4 ] 14197316-28379460 | [ 8 ] 15172-14197316 |************************************************** [ 633 ] Storage Throughput = excellent ( 1376.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020418 bp ( 40019018 non ambiguous ) - Num Contigs Represented = 130 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:54 (hh:mm:ss) Elapsed Time Round Time: 00:26:46 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2218 repeats masked totaling 876680 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013558 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10013158 bp After Masking: 8116478 bp Masked: 18.94 % -- Input Database Coverage: 10013558 bp out of 1181506259 bp ( 0.85 % ) Sampling Time: 00:12:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:20 (hh:mm:ss) Elapsed Time, 498 HSPs Collected Number of families returned by RECON: 200 Round Time: 00:20:09 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7279 repeats masked totaling 2621585 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006857 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30005857 bp After Masking: 24528527 bp Masked: 18.25 % -- Input Database Coverage: 40020415 bp out of 1181506259 bp ( 3.39 % ) Sampling Time: 00:37:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:32:08 (hh:mm:ss) Elapsed Time, 9266 HSPs Collected Number of families returned by RECON: 1171 Round Time: 01:10:25 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:40:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22782 repeats masked totaling 8349912 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036380 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 90032880 bp After Masking: 73680931 bp Masked: 18.16 % -- Input Database Coverage: 130056795 bp out of 1181506259 bp ( 11.01 % ) Sampling Time: 01:45:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 03:20:31 (hh:mm:ss) Elapsed Time, 61251 HSPs Collected Number of families returned by RECON: 6873 Round Time: 05:08:01 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 05:18:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75595 repeats masked totaling 27310915 bp(s). - TE Masking time 00:03:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041492 bp Num Contigs Represented = 376 Non ambiguous bp: Initial: 270033792 bp After Masking: 218471360 bp Masked: 19.09 % -- Input Database Coverage: 400098287 bp out of 1181506259 bp ( 33.86 % ) Sampling Time: 05:33:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23368866 Comparison Time: 26:06:48 (hh:mm:ss) Elapsed Time, 228819 HSPs Collected Number of families returned by RECON: 45818 Round Time: 32:02:15 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatScout/RECON discovery complete: 366 families found Classification Time: 00:25:19 (hh:mm:ss) Elapsed Time Program Time: 39:32:55 (hh:mm:ss) Elapsed Time