RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Jhj6jI/RM_29943.SunJul141947012024 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: 1721011620 Database = /dev/shm/rModeler.Jhj6jI/GCF_005281545.1_ASM528154v1 - Sequences = 4201 - Bases = 1087415941 - N50 = 46513705 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 53891372-57740692 | [ 1 ] 50042052-53891371 | [ 2 ] 46192732-50042051 | [ 8 ] 42343412-46192731 | [ 6 ] 38494093-42343412 | [ 5 ] 34644773-38494092 | [ 1 ] 30795453-34644772 | [ ] 26946133-30795452 | [ ] 23096813-26946132 | [ ] 19247494-23096813 | [ 1 ] 15398174-19247493 | [ ] 11548854-15398173 | [ ] 7699534-11548853 | [ ] 3850214-7699533 | [ ] 895-3850214 |************************************************* [ 4177 ] Storage Throughput = excellent ( 1049.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41662291 bp ( 40009265 non ambiguous ) - Num Contigs Represented = 191 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:42 (hh:mm:ss) Elapsed Time Round Time: 00:25:21 (hh:mm:ss) Elapsed Time : 1001 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16712 repeats masked totaling 2727820 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10486491 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10034507 bp After Masking: 7137382 bp Masked: 28.87 % -- Input Database Coverage: 10486491 bp out of 1087415941 bp ( 0.96 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42486 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 15359 HSPs Collected Number of families returned by RECON: 2068 Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53136 repeats masked totaling 8499668 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31215796 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 30014754 bp After Masking: 21000320 bp Masked: 30.03 % -- Input Database Coverage: 41702287 bp out of 1087415941 bp ( 3.83 % ) Sampling Time: 00:02:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 406351 Comparison Time: 00:34:05 (hh:mm:ss) Elapsed Time, 78709 HSPs Collected Number of families returned by RECON: 6533 Round Time: 00:39:58 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 178851 repeats masked totaling 29144388 bp(s). - TE Masking time 00:02:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 93405407 bp Num Contigs Represented = 394 Non ambiguous bp: Initial: 90027710 bp After Masking: 59263517 bp Masked: 34.17 % -- Input Database Coverage: 135107694 bp out of 1087415941 bp ( 12.42 % ) Sampling Time: 00:08:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3563115 Comparison Time: 03:35:07 (hh:mm:ss) Elapsed Time, 383948 HSPs Collected Number of families returned by RECON: 18250 Round Time: 04:05:39 (hh:mm:ss) Elapsed Time : 766 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 626699 repeats masked totaling 105458140 bp(s). - TE Masking time 00:15:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 280281497 bp Num Contigs Represented = 1120 Non ambiguous bp: Initial: 270009537 bp After Masking: 160016278 bp Masked: 40.74 % -- Input Database Coverage: 415389191 bp out of 1087415941 bp ( 38.20 % ) Sampling Time: 00:33:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31916055 Comparison Time: 28:45:56 (hh:mm:ss) Elapsed Time, 923519 HSPs Collected Number of families returned by RECON: 57085 Round Time: 31:50:59 (hh:mm:ss) Elapsed Time : 1596 families discovered. RepeatScout/RECON discovery complete: 3621 families found Classification Time: 02:04:11 (hh:mm:ss) Elapsed Time Program Time: 39:14:18 (hh:mm:ss) Elapsed Time