RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QJ5891/RM_6671.SatDec22156482023 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: 1701583007 Database = /dev/shm/rModeler.QJ5891/GCA_030435715.1_mOchPri1.hap2 - Sequences = 6117 - Bases = 2534779560 - N50 = 71356865 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 155248438-166336790 | [ 2 ] 144160087-155248438 | [ ] 133071735-144160086 | [ ] 121983384-133071735 | [ ] 110895033-121983384 | [ 1 ] 99806681-110895032 | [ 2 ] 88718330-99806681 | [ ] 77629978-88718329 | [ 5 ] 66541627-77629978 | [ 3 ] 55453276-66541627 | [ 3 ] 44364924-55453275 | [ 4 ] 33276573-44364924 | [ 5 ] 22188221-33276572 | [ 4 ] 11099870-22188221 | [ 3 ] 11519-11099870 |************************************************** [ 6085 ] Storage Throughput = excellent ( 1100.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040058 bp ( 40039258 non ambiguous ) - Num Contigs Represented = 265 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:08 (hh:mm:ss) Elapsed Time Round Time: 01:13:18 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9271 repeats masked totaling 2288227 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027111 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 10026911 bp After Masking: 5690615 bp Masked: 43.25 % -- Input Database Coverage: 10027111 bp out of 2534779560 bp ( 0.40 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 1719 HSPs Collected Number of families returned by RECON: 345 Round Time: 00:07:42 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29089 repeats masked totaling 7034663 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012867 bp Num Contigs Represented = 206 Non ambiguous bp: Initial: 30012267 bp After Masking: 16503764 bp Masked: 45.01 % -- Input Database Coverage: 40039978 bp out of 2534779560 bp ( 1.58 % ) Sampling Time: 00:04:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:24:03 (hh:mm:ss) Elapsed Time, 17245 HSPs Collected Number of families returned by RECON: 1453 Round Time: 00:28:48 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 95089 repeats masked totaling 23245773 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005303 bp Num Contigs Represented = 529 Non ambiguous bp: Initial: 90003503 bp After Masking: 48653599 bp Masked: 45.94 % -- Input Database Coverage: 130045281 bp out of 2534779560 bp ( 5.13 % ) Sampling Time: 00:15:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2764776 Comparison Time: 02:37:56 (hh:mm:ss) Elapsed Time, 46319 HSPs Collected Number of families returned by RECON: 5309 Round Time: 02:56:24 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 304694 repeats masked totaling 73392674 bp(s). - TE Masking time 00:05:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046962 bp Num Contigs Represented = 1414 Non ambiguous bp: Initial: 270037162 bp After Masking: 143468590 bp Masked: 46.87 % -- Input Database Coverage: 400092243 bp out of 2534779560 bp ( 15.78 % ) Sampling Time: 00:36:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25031350 Comparison Time: 19:44:58 (hh:mm:ss) Elapsed Time, 201885 HSPs Collected Number of families returned by RECON: 24576 Round Time: 20:36:14 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatScout/RECON discovery complete: 574 families found Classification Time: 00:34:01 (hh:mm:ss) Elapsed Time Program Time: 25:56:27 (hh:mm:ss) Elapsed Time