RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.AVfm3R/RM_3971495.WedDec181110462024 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: 1734549045 Database = /data/tmp/rModeler.AVfm3R/GCA_039906525.1_mPseCra1.hap2 - Sequences = 416 - Bases = 2678530964 - N50 = 110511256 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 199707683-213971634 | [ 1 ] 185443732-199707682 | [ 1 ] 171179782-185443732 | [ 1 ] 156915831-171179781 | [ ] 142651881-156915831 | [ 2 ] 128387930-142651880 | [ 1 ] 114123979-128387929 | [ 1 ] 99860029-114123979 | [ 4 ] 85596078-99860028 | [ 5 ] 71332128-85596078 | [ 2 ] 57068177-71332127 | [ 2 ] 42804226-57068176 | [ ] 28540276-42804226 | [ 1 ] 14276325-28540275 | [ 1 ] 12375-14276325 |************************************************** [ 394 ] Storage Throughput = excellent ( 1090.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40375643 bp ( 40036585 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:07 (hh:mm:ss) Elapsed Time Round Time: 00:33:48 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9496 repeats masked totaling 3027468 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10047627 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10007569 bp After Masking: 6696470 bp Masked: 33.09 % -- Input Database Coverage: 10047627 bp out of 2678530964 bp ( 0.38 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:09:08 (hh:mm:ss) Elapsed Time, 737904 HSPs Collected Number of families returned by RECON: 711 Round Time: 00:31:45 (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 : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37323 repeats masked totaling 11264516 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30327936 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 30028936 bp After Masking: 18219406 bp Masked: 39.33 % -- Input Database Coverage: 40375563 bp out of 2678530964 bp ( 1.51 % ) Sampling Time: 00:03:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:27:30 (hh:mm:ss) Elapsed Time, 58915 HSPs Collected Number of families returned by RECON: 2277 Round Time: 00:34:29 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121504 repeats masked totaling 35289551 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90683526 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 90010982 bp After Masking: 52456909 bp Masked: 41.72 % -- Input Database Coverage: 131059089 bp out of 2678530964 bp ( 4.89 % ) Sampling Time: 00:11:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:35:01 (hh:mm:ss) Elapsed Time, 515951 HSPs Collected Number of families returned by RECON: 7634 Round Time: 02:57:59 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 403918 repeats masked totaling 112960492 bp(s). - TE Masking time 00:04:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272702943 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 270035287 bp After Masking: 150413159 bp Masked: 44.30 % -- Input Database Coverage: 403762032 bp out of 2678530964 bp ( 15.07 % ) Sampling Time: 00:33:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23416746 Comparison Time: 16:14:55 (hh:mm:ss) Elapsed Time, 3063301 HSPs Collected Number of families returned by RECON: 28503 Round Time: 17:34:09 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatScout/RECON discovery complete: 727 families found Classification Time: 00:31:43 (hh:mm:ss) Elapsed Time Program Time: 22:43:53 (hh:mm:ss) Elapsed Time