RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lZELGK/RM_3091416.WedJul31026012024 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: 1720027560 Database = /dev/shm/rModeler.lZELGK/GCF_902827165.1_fTreBer1.1 - Sequences = 864 - Bases = 867125071 - N50 = 8748290 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29399222-31498804 | [ 1 ] 27299641-29399222 | [ 2 ] 25200060-27299641 | [ ] 23100478-25200059 | [ ] 21000897-23100478 | [ 2 ] 18901316-21000897 | [ 4 ] 16801735-18901316 | [ 1 ] 14702153-16801734 | [ 3 ] 12602572-14702153 | [ 5 ] 10502991-12602572 | [ 2 ] 8403410-10502991 | [ 9 ] 6303828-8403409 | [ 6 ] 4204247-6303828 |* [ 18 ] 2104666-4204247 |* [ 30 ] 5085-2104666 |************************************************** [ 781 ] Storage Throughput = good ( 881.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015383 bp ( 40010556 non ambiguous ) - Num Contigs Represented = 235 - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:46 (hh:mm:ss) Elapsed Time Round Time: 00:24:54 (hh:mm:ss) Elapsed Time : 772 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10753 repeats masked totaling 2829148 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027076 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 10025784 bp After Masking: 6662984 bp Masked: 33.54 % -- Input Database Coverage: 10027076 bp out of 867125071 bp ( 1.16 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:04:35 (hh:mm:ss) Elapsed Time, 4084 HSPs Collected Number of families returned by RECON: 1000 Round Time: 00:06:19 (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 : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34237 repeats masked totaling 8949648 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028208 bp Num Contigs Represented = 207 Non ambiguous bp: Initial: 30024673 bp After Masking: 19504849 bp Masked: 35.04 % -- Input Database Coverage: 40055284 bp out of 867125071 bp ( 4.62 % ) Sampling Time: 00:04:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:23:43 (hh:mm:ss) Elapsed Time, 30823 HSPs Collected Number of families returned by RECON: 3524 Round Time: 00:29:14 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107124 repeats masked totaling 27091020 bp(s). - TE Masking time 00:03:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048679 bp Num Contigs Represented = 337 Non ambiguous bp: Initial: 90037379 bp After Masking: 58060011 bp Masked: 35.52 % -- Input Database Coverage: 130103963 bp out of 867125071 bp ( 15.00 % ) Sampling Time: 00:14:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2662278 Comparison Time: 02:40:09 (hh:mm:ss) Elapsed Time, 230958 HSPs Collected Number of families returned by RECON: 11909 Round Time: 03:03:51 (hh:mm:ss) Elapsed Time : 444 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 372457 repeats masked totaling 93732954 bp(s). - TE Masking time 00:14:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046402 bp Num Contigs Represented = 531 Non ambiguous bp: Initial: 270008874 bp After Masking: 161493899 bp Masked: 40.19 % -- Input Database Coverage: 400150365 bp out of 867125071 bp ( 46.15 % ) Sampling Time: 00:49:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23663760 Comparison Time: 19:04:11 (hh:mm:ss) Elapsed Time, 705719 HSPs Collected Number of families returned by RECON: 43711 Round Time: 20:52:24 (hh:mm:ss) Elapsed Time : 1028 families discovered. RepeatScout/RECON discovery complete: 2310 families found Classification Time: 02:19:53 (hh:mm:ss) Elapsed Time Program Time: 27:16:36 (hh:mm:ss) Elapsed Time