RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.nyB8Jn/RM_3644347.SunNov171026392024 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: 1731867998 Database = /scratch/tmp/rModeler.nyB8Jn/GCA_039880945.1_mMolNig1.hap1 - Sequences = 366 - Bases = 2567103348 - N50 = 117666054 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 271281030-290657952 | [ 1 ] 251904108-271281029 | [ ] 232527186-251904107 | [ ] 213150264-232527185 | [ ] 193773343-213150264 | [ ] 174396421-193773342 | [ ] 155019499-174396420 | [ ] 135642577-155019498 | [ 2 ] 116265655-135642576 | [ 5 ] 96888734-116265655 | [ 6 ] 77511812-96888733 | [ 2 ] 58134890-77511811 | [ 4 ] 38757968-58134889 | [ 2 ] 19381046-38757967 | [ 2 ] 4125-19381046 |************************************************** [ 342 ] Storage Throughput = excellent ( 1459.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030423 bp ( 40030323 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:29 (hh:mm:ss) Elapsed Time Round Time: 00:16:18 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11320 repeats masked totaling 3154072 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015435 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10015335 bp After Masking: 6739321 bp Masked: 32.71 % -- Input Database Coverage: 10015435 bp out of 2567103348 bp ( 0.39 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 6885 HSPs Collected Number of families returned by RECON: 780 Round Time: 00:12:42 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35834 repeats masked totaling 11033498 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014984 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30014984 bp After Masking: 18594020 bp Masked: 38.05 % -- Input Database Coverage: 40030419 bp out of 2567103348 bp ( 1.56 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:13:22 (hh:mm:ss) Elapsed Time, 22651 HSPs Collected Number of families returned by RECON: 2087 Round Time: 00:15:47 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113607 repeats masked totaling 33634875 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025043 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90024543 bp After Masking: 55030376 bp Masked: 38.87 % -- Input Database Coverage: 130055462 bp out of 2567103348 bp ( 5.07 % ) Sampling Time: 00:06:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:05:23 (hh:mm:ss) Elapsed Time, 100671 HSPs Collected Number of families returned by RECON: 7118 Round Time: 01:14:15 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 385940 repeats masked totaling 109173590 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007817 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270006417 bp After Masking: 156940868 bp Masked: 41.88 % -- Input Database Coverage: 400063279 bp out of 2567103348 bp ( 15.58 % ) Sampling Time: 00:18:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 08:22:24 (hh:mm:ss) Elapsed Time, 317325 HSPs Collected Number of families returned by RECON: 30535 Round Time: 08:51:58 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatScout/RECON discovery complete: 874 families found Classification Time: 00:20:50 (hh:mm:ss) Elapsed Time Program Time: 11:11:50 (hh:mm:ss) Elapsed Time