RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Wj8e97/RM_15462.TueJul231853112024 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: 1721785984 Database = /dev/shm/rModeler.Wj8e97/GCF_018812025.1_ASM1881202v1 - Sequences = 243 - Bases = 1109888616 - N50 = 44064265 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 70804355-75861420 | [ 1 ] 65747290-70804354 | [ ] 60690225-65747289 | [ 2 ] 55633161-60690225 | [ 2 ] 50576096-55633160 | [ 1 ] 45519031-50576095 | [ 2 ] 40461966-45519030 |* [ 7 ] 35404902-40461966 | [ 4 ] 30347837-35404901 | [ 4 ] 25290772-30347836 | [ 1 ] 20233707-25290771 | [ ] 15176643-20233707 | [ ] 10119578-15176642 | [ ] 5062513-10119577 | [ ] 5449-5062513 |************************************************** [ 219 ] Storage Throughput = excellent ( 1020.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40111889 bp ( 40036463 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:15 (hh:mm:ss) Elapsed Time Round Time: 01:19:52 (hh:mm:ss) Elapsed Time : 1244 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18289 repeats masked totaling 3925083 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023398 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10013559 bp After Masking: 5741617 bp Masked: 42.66 % -- Input Database Coverage: 10023398 bp out of 1109888616 bp ( 0.90 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 01:04:42 (hh:mm:ss) Elapsed Time, 9229 HSPs Collected Number of families returned by RECON: 1702 Round Time: 01:09:34 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55966 repeats masked totaling 12188674 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30088411 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30022824 bp After Masking: 16769712 bp Masked: 44.14 % -- Input Database Coverage: 40111809 bp out of 1109888616 bp ( 3.61 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 02:52:38 (hh:mm:ss) Elapsed Time, 55835 HSPs Collected Number of families returned by RECON: 5372 Round Time: 03:05:33 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179576 repeats masked totaling 37870632 bp(s). - TE Masking time 00:04:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90178795 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90037798 bp After Masking: 49113394 bp Masked: 45.45 % -- Input Database Coverage: 130290604 bp out of 1109888616 bp ( 11.74 % ) Sampling Time: 00:13:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 09:55:12 (hh:mm:ss) Elapsed Time, 367689 HSPs Collected Number of families returned by RECON: 15270 Round Time: 10:45:39 (hh:mm:ss) Elapsed Time : 684 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 620412 repeats masked totaling 131253952 bp(s). - TE Masking time 00:22:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270427863 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 270020523 bp After Masking: 129483616 bp Masked: 52.05 % -- Input Database Coverage: 400718467 bp out of 1109888616 bp ( 36.10 % ) Sampling Time: 00:49:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23021505 Comparison Time: 49:46:24 (hh:mm:ss) Elapsed Time, 971241 HSPs Collected Number of families returned by RECON: 43335 Round Time: 53:11:28 (hh:mm:ss) Elapsed Time : 1555 families discovered. RepeatScout/RECON discovery complete: 3648 families found Classification Time: 02:36:46 (hh:mm:ss) Elapsed Time Program Time: 72:08:52 (hh:mm:ss) Elapsed Time