RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.6I3ZHd/RM_2387773.MonNov181950012024 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: 1731988200 Database = /scratch/tmp/rModeler.6I3ZHd/GCA_964106915.1_rPodGai1.hap1.1 - Sequences = 211 - Bases = 1514643635 - N50 = 99788972 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 129595766-138852535 | [ 1 ] 120338997-129595766 | [ 2 ] 111082228-120338997 | [ ] 101825459-111082228 | [ 1 ] 92568690-101825459 | [ 2 ] 83311921-92568690 | [ 2 ] 74055152-83311921 | [ 2 ] 64798383-74055152 | [ 1 ] 55541614-64798383 | [ 2 ] 46284845-55541614 | [ 3 ] 37028076-46284845 | [ 2 ] 27771307-37028076 | [ 1 ] 18514538-27771307 | [ ] 9257769-18514538 | [ 1 ] 1000-9257769 |************************************************** [ 191 ] Storage Throughput = excellent ( 1514.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020546 bp ( 40016076 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:05 (hh:mm:ss) Elapsed Time Round Time: 00:11:05 (hh:mm:ss) Elapsed Time : 527 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16966 repeats masked totaling 3157515 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003841 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10002841 bp After Masking: 6579767 bp Masked: 34.22 % -- Input Database Coverage: 10003841 bp out of 1514643635 bp ( 0.66 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 9898 HSPs Collected Number of families returned by RECON: 1319 Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53968 repeats masked totaling 10026046 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016625 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30013155 bp After Masking: 18558059 bp Masked: 38.17 % -- Input Database Coverage: 40020466 bp out of 1514643635 bp ( 2.64 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:10:58 (hh:mm:ss) Elapsed Time, 48867 HSPs Collected Number of families returned by RECON: 4295 Round Time: 00:13:15 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177374 repeats masked totaling 32514051 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029042 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90015624 bp After Masking: 54362109 bp Masked: 39.61 % -- Input Database Coverage: 130049508 bp out of 1514643635 bp ( 8.59 % ) Sampling Time: 00:04:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 01:01:35 (hh:mm:ss) Elapsed Time, 198844 HSPs Collected Number of families returned by RECON: 13947 Round Time: 01:10:19 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 598383 repeats masked totaling 107718912 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064202 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 270036802 bp After Masking: 152828125 bp Masked: 43.40 % -- Input Database Coverage: 400113710 bp out of 1514643635 bp ( 26.42 % ) Sampling Time: 00:14:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 07:08:33 (hh:mm:ss) Elapsed Time, 490574 HSPs Collected Number of families returned by RECON: 47622 Round Time: 07:49:13 (hh:mm:ss) Elapsed Time : 1018 families discovered. RepeatScout/RECON discovery complete: 2152 families found Classification Time: 00:31:40 (hh:mm:ss) Elapsed Time Program Time: 09:59:02 (hh:mm:ss) Elapsed Time