RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Cd6htS/RM_27357.WedDec60338342023 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: 1701862711 Database = /dev/shm/rModeler.Cd6htS/GCA_949316315.1_mMusMuc1.1 - Sequences = 179 - Bases = 2770968735 - N50 = 146218837 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 186785950-200127270 | [ 1 ] 173444631-186785950 | [ 1 ] 160103312-173444631 | [ 3 ] 146761993-160103312 | [ 2 ] 133420674-146761993 | [ 1 ] 120079354-133420673 |* [ 5 ] 106738035-120079354 | [ 2 ] 93396716-106738035 | [ 3 ] 80055397-93396716 | [ 1 ] 66714078-80055397 | [ ] 53372758-66714077 | [ 1 ] 40031439-53372758 | [ ] 26690120-40031439 | [ ] 13348801-26690120 | [ ] 7482-13348801 |************************************************** [ 159 ] Storage Throughput = excellent ( 1182.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016132 bp ( 40015932 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:01 (hh:mm:ss) Elapsed Time Round Time: 00:33:07 (hh:mm:ss) Elapsed Time : 271 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11320 repeats masked totaling 2818425 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002619 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10002619 bp After Masking: 6036485 bp Masked: 39.65 % -- Input Database Coverage: 10002619 bp out of 2770968735 bp ( 0.36 % ) Sampling Time: 00:02:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:01 (hh:mm:ss) Elapsed Time, 5404 HSPs Collected Number of families returned by RECON: 681 Round Time: 00:08:15 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37311 repeats masked totaling 9327249 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013508 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30013308 bp After Masking: 18313354 bp Masked: 38.98 % -- Input Database Coverage: 40016127 bp out of 2770968735 bp ( 1.44 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:24 (hh:mm:ss) Elapsed Time, 18180 HSPs Collected Number of families returned by RECON: 2188 Round Time: 00:32:54 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113833 repeats masked totaling 27577530 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040085 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90038085 bp After Masking: 54073747 bp Masked: 39.94 % -- Input Database Coverage: 130056212 bp out of 2770968735 bp ( 4.69 % ) Sampling Time: 00:22:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:43:56 (hh:mm:ss) Elapsed Time, 78794 HSPs Collected Number of families returned by RECON: 8385 Round Time: 04:10:22 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:47:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 397580 repeats masked totaling 91835622 bp(s). - TE Masking time 00:06:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038123 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 270035723 bp After Masking: 153749126 bp Masked: 43.06 % -- Input Database Coverage: 400094335 bp out of 2770968735 bp ( 14.44 % ) Sampling Time: 01:13:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 22:43:25 (hh:mm:ss) Elapsed Time, 210576 HSPs Collected Number of families returned by RECON: 30906 Round Time: 24:23:09 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatScout/RECON discovery complete: 853 families found Classification Time: 00:37:02 (hh:mm:ss) Elapsed Time Program Time: 30:24:49 (hh:mm:ss) Elapsed Time