RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xChwdx/RM_3025052.ThuMay111013082023 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: 1683825188 Database = /dev/shm/rModeler.xChwdx/GCA_028020825.1_bPodStr1.pri - Sequences = 1038 - Bases = 1271141449 - N50 = 63752180 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 165669231-177501524 | [ 1 ] 153836939-165669231 | [ ] 142004647-153836939 | [ ] 130172354-142004646 | [ ] 118340062-130172354 | [ 1 ] 106507770-118340062 | [ ] 94675477-106507769 | [ 1 ] 82843185-94675477 | [ ] 71010893-82843185 | [ 2 ] 59178600-71010892 | [ 1 ] 47346308-59178600 | [ 1 ] 35514016-47346308 | [ 3 ] 23681723-35514015 | [ 2 ] 11849431-23681723 | [ 12 ] 17139-11849431 |************************************************** [ 1014 ] Storage Throughput = excellent ( 1015.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40067015 bp ( 40025802 non ambiguous ) - Num Contigs Represented = 125 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:05 (hh:mm:ss) Elapsed Time Round Time: 00:28:13 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1954 repeats masked totaling 861077 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025634 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10025621 bp After Masking: 8223904 bp Masked: 17.97 % -- Input Database Coverage: 10025634 bp out of 1271141449 bp ( 0.79 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 520 HSPs Collected Number of families returned by RECON: 221 Round Time: 00:10:22 (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 : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5603 repeats masked totaling 2339059 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041301 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30000101 bp After Masking: 24589262 bp Masked: 18.04 % -- Input Database Coverage: 40066935 bp out of 1271141449 bp ( 3.15 % ) Sampling Time: 00:11:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:34:42 (hh:mm:ss) Elapsed Time, 4697 HSPs Collected Number of families returned by RECON: 1317 Round Time: 00:48:17 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17988 repeats masked totaling 7228239 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90198224 bp Num Contigs Represented = 222 Non ambiguous bp: Initial: 90005485 bp After Masking: 74878013 bp Masked: 16.81 % -- Input Database Coverage: 130265159 bp out of 1271141449 bp ( 10.25 % ) Sampling Time: 00:36:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2646150 Comparison Time: 03:54:00 (hh:mm:ss) Elapsed Time, 32085 HSPs Collected Number of families returned by RECON: 7991 Round Time: 04:34:43 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:11:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62757 repeats masked totaling 24151813 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270493073 bp Num Contigs Represented = 469 Non ambiguous bp: Initial: 270026834 bp After Masking: 222259983 bp Masked: 17.69 % -- Input Database Coverage: 400758232 bp out of 1271141449 bp ( 31.53 % ) Sampling Time: 02:25:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23595015 Comparison Time: 27:27:22 (hh:mm:ss) Elapsed Time, 156912 HSPs Collected Number of families returned by RECON: 54075 Round Time: 30:35:58 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:32:52 (hh:mm:ss) Elapsed Time Program Time: 37:10:25 (hh:mm:ss) Elapsed Time