RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BqjaJO/RM_27676.SunJan140105412024 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: 1705223137 Database = /dev/shm/rModeler.BqjaJO/GCA_031885435.1_bPasSan2.pri - Sequences = 110 - Bases = 1270940266 - N50 = 73843927 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146645341-157118810 | [ 1 ] 136171872-146645340 | [ ] 125698403-136171871 | [ ] 115224934-125698402 |* [ 2 ] 104751466-115224934 | [ ] 94277997-104751465 | [ ] 83804528-94277996 | [ ] 73331059-83804527 |* [ 3 ] 62857590-73331058 | [ 1 ] 52384122-62857590 | [ ] 41910653-52384121 | [ 1 ] 31437184-41910652 |* [ 3 ] 20963715-31437183 |** [ 4 ] 10490246-20963714 |******* [ 13 ] 16778-10490246 |************************************************** [ 82 ] Storage Throughput = excellent ( 1134.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40074359 bp ( 40033432 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:42 (hh:mm:ss) Elapsed Time Round Time: 00:39:05 (hh:mm:ss) Elapsed Time : 248 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3646 repeats masked totaling 1625098 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040501 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10000500 bp After Masking: 7790323 bp Masked: 22.10 % -- Input Database Coverage: 10040501 bp out of 1270940266 bp ( 0.79 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:33 (hh:mm:ss) Elapsed Time, 988 HSPs Collected Number of families returned by RECON: 296 Round Time: 00:12:12 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11590 repeats masked totaling 4300155 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033778 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30032852 bp After Masking: 23599099 bp Masked: 21.42 % -- Input Database Coverage: 40074279 bp out of 1270940266 bp ( 3.15 % ) Sampling Time: 00:04:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:36:31 (hh:mm:ss) Elapsed Time, 10066 HSPs Collected Number of families returned by RECON: 1695 Round Time: 00:41:38 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36125 repeats masked totaling 13196122 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90172379 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90038785 bp After Masking: 70338230 bp Masked: 21.88 % -- Input Database Coverage: 130246658 bp out of 1270940266 bp ( 10.25 % ) Sampling Time: 00:13:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 04:40:12 (hh:mm:ss) Elapsed Time, 77152 HSPs Collected Number of families returned by RECON: 10012 Round Time: 04:59:12 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120693 repeats masked totaling 43339337 bp(s). - TE Masking time 00:08:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270590111 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270021768 bp After Masking: 206344834 bp Masked: 23.58 % -- Input Database Coverage: 400836769 bp out of 1270940266 bp ( 31.54 % ) Sampling Time: 00:44:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 35:05:45 (hh:mm:ss) Elapsed Time, 356517 HSPs Collected Number of families returned by RECON: 62137 Round Time: 36:57:40 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatScout/RECON discovery complete: 752 families found Classification Time: 01:04:04 (hh:mm:ss) Elapsed Time Program Time: 44:33:51 (hh:mm:ss) Elapsed Time