RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PlKoSa/RM_23013.MonJun241511412024 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: 1719267099 Database = /dev/shm/rModeler.PlKoSa/GCF_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 ( 1226.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40089359 bp ( 40012430 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:15:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:59 (hh:mm:ss) Elapsed Time Round Time: 00:59:23 (hh:mm:ss) Elapsed Time : 806 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:02 (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... 14572 repeats masked totaling 5293842 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000522 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 9999922 bp After Masking: 3189888 bp Masked: 68.10 % -- Input Database Coverage: 10000522 bp out of 8872758793 bp ( 0.11 % ) Sampling Time: 00:05:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 37943 HSPs Collected Number of families returned by RECON: 968 Round Time: 00:12:47 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:11:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45011 repeats masked totaling 17108554 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30088757 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 30012428 bp After Masking: 8739357 bp Masked: 70.88 % -- Input Database Coverage: 40089279 bp out of 8872758793 bp ( 0.45 % ) Sampling Time: 00:17:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:17:46 (hh:mm:ss) Elapsed Time, 92477 HSPs Collected Number of families returned by RECON: 3311 Round Time: 00:37:06 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:34:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138378 repeats masked totaling 52496147 bp(s). - TE Masking time 00:03:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90374156 bp Num Contigs Represented = 191 Non ambiguous bp: Initial: 90011917 bp After Masking: 24006573 bp Masked: 73.33 % -- Input Database Coverage: 130463435 bp out of 8872758793 bp ( 1.47 % ) Sampling Time: 00:54:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:28:57 (hh:mm:ss) Elapsed Time, 223954 HSPs Collected Number of families returned by RECON: 8855 Round Time: 02:31:14 (hh:mm:ss) Elapsed Time : 352 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:46:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459845 repeats masked totaling 169800654 bp(s). - TE Masking time 00:12:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270452745 bp Num Contigs Represented = 462 Non ambiguous bp: Initial: 270009514 bp After Masking: 61266731 bp Masked: 77.31 % -- Input Database Coverage: 400916180 bp out of 8872758793 bp ( 4.52 % ) Sampling Time: 02:43:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 09:09:12 (hh:mm:ss) Elapsed Time, 855275 HSPs Collected Number of families returned by RECON: 23533 Round Time: 12:51:06 (hh:mm:ss) Elapsed Time : 1112 families discovered. RepeatScout/RECON discovery complete: 2354 families found Classification Time: 01:50:31 (hh:mm:ss) Elapsed Time Program Time: 19:02:07 (hh:mm:ss) Elapsed Time