RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1r000j/RM_414140.TueApr221702042025 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: 1745366523 Database = /dev/shm/rModeler.1r000j/GCA_048126345.1_UniMelb_NotTyph_v1.0 - Sequences = 693 - Bases = 3845140558 - N50 = 641257124 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 710650667-761411215 | [ 1 ] 659890119-710650666 | [ ] 609129572-659890119 | [ 1 ] 558369024-609129571 | [ ] 507608476-558369023 | [ ] 456847929-507608476 | [ 1 ] 406087381-456847928 | [ ] 355326833-406087380 | [ 1 ] 304566286-355326833 | [ 3 ] 253805738-304566285 | [ 1 ] 203045190-253805737 | [ 1 ] 152284643-203045190 | [ ] 101524095-152284642 | [ ] 50763547-101524094 | [ 1 ] 3000-50763547 |************************************************** [ 683 ] Storage Throughput = excellent ( 1799.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006622 bp ( 40006122 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:04:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:05 (hh:mm:ss) Elapsed Time Round Time: 00:18:37 (hh:mm:ss) Elapsed Time : 377 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:13 (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... 21467 repeats masked totaling 4475306 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002488 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 10002488 bp After Masking: 5406751 bp Masked: 45.95 % -- Input Database Coverage: 10002488 bp out of 3845140558 bp ( 0.26 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 10736 HSPs Collected Number of families returned by RECON: 1038 Round Time: 00:04:55 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68442 repeats masked totaling 14675583 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004054 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30003554 bp After Masking: 14955461 bp Masked: 50.15 % -- Input Database Coverage: 40006542 bp out of 3845140558 bp ( 1.04 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:34 (hh:mm:ss) Elapsed Time, 26520 HSPs Collected Number of families returned by RECON: 2957 Round Time: 00:17:45 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:10:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 215471 repeats masked totaling 47879982 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90053052 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90017637 bp After Masking: 40768865 bp Masked: 54.71 % -- Input Database Coverage: 130059594 bp out of 3845140558 bp ( 3.38 % ) Sampling Time: 00:14:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 00:58:01 (hh:mm:ss) Elapsed Time, 70968 HSPs Collected Number of families returned by RECON: 7994 Round Time: 01:13:25 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:32:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 693473 repeats masked totaling 152409550 bp(s). - TE Masking time 00:03:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014402 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 270000636 bp After Masking: 114045853 bp Masked: 57.76 % -- Input Database Coverage: 400073996 bp out of 3845140558 bp ( 10.40 % ) Sampling Time: 00:43:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 06:21:39 (hh:mm:ss) Elapsed Time, 230820 HSPs Collected Number of families returned by RECON: 28475 Round Time: 07:13:07 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatScout/RECON discovery complete: 1131 families found Classification Time: 00:19:57 (hh:mm:ss) Elapsed Time Program Time: 09:27:46 (hh:mm:ss) Elapsed Time