RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IdshTG/RM_17200.SatNov252109352023 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: 1700975372 Database = /dev/shm/rModeler.IdshTG/GCA_028390025.1_aPseCor3.hap2 - Sequences = 3127 - Bases = 8872758793 - N50 = 852354006 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1168083896-1251518389 | [ 1 ] 1084649403-1168083895 | [ ] 1001214911-1084649403 | [ 1 ] 917780418-1001214910 | [ 1 ] 834345926-917780418 | [ 2 ] 750911433-834345925 | [ 1 ] 667476940-750911432 | [ ] 584042448-667476940 | [ ] 500607955-584042447 | [ 1 ] 417173463-500607955 | [ 2 ] 333738970-417173462 | [ 2 ] 250304477-333738969 | [ ] 166869985-250304477 | [ 1 ] 83435492-166869984 | [ ] 1000-83435492 |************************************************** [ 3115 ] Storage Throughput = excellent ( 1165.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40077627 bp ( 40030042 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:15:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:38 (hh:mm:ss) Elapsed Time Round Time: 00:57:50 (hh:mm:ss) Elapsed Time : 788 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:56 (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... 14308 repeats masked totaling 5468024 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011011 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10010811 bp After Masking: 3018737 bp Masked: 69.85 % -- Input Database Coverage: 10011011 bp out of 8872758793 bp ( 0.11 % ) Sampling Time: 00:06:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 6468 HSPs Collected Number of families returned by RECON: 910 Round Time: 00:11:37 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:12:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45004 repeats masked totaling 17308222 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30066615 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30019230 bp After Masking: 8531609 bp Masked: 71.58 % -- Input Database Coverage: 40077626 bp out of 8872758793 bp ( 0.45 % ) Sampling Time: 00:18:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:21:02 (hh:mm:ss) Elapsed Time, 39926 HSPs Collected Number of families returned by RECON: 3038 Round Time: 00:43:22 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:35:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138134 repeats masked totaling 52273875 bp(s). - TE Masking time 00:03:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90308315 bp Num Contigs Represented = 178 Non ambiguous bp: Initial: 90008650 bp After Masking: 25040075 bp Masked: 72.18 % -- Input Database Coverage: 130385941 bp out of 8872758793 bp ( 1.47 % ) Sampling Time: 00:54:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:40:01 (hh:mm:ss) Elapsed Time, 261563 HSPs Collected Number of families returned by RECON: 9111 Round Time: 02:57:49 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:44:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 454661 repeats masked totaling 170317451 bp(s). - TE Masking time 00:13:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270855866 bp Num Contigs Represented = 454 Non ambiguous bp: Initial: 270002289 bp After Masking: 61210062 bp Masked: 77.33 % -- Input Database Coverage: 401241807 bp out of 8872758793 bp ( 4.52 % ) Sampling Time: 02:44:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23273253 Comparison Time: 09:44:14 (hh:mm:ss) Elapsed Time, 858918 HSPs Collected Number of families returned by RECON: 23127 Round Time: 13:11:13 (hh:mm:ss) Elapsed Time : 1102 families discovered. RepeatScout/RECON discovery complete: 2336 families found Classification Time: 01:56:57 (hh:mm:ss) Elapsed Time Program Time: 19:58:48 (hh:mm:ss) Elapsed Time