RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.cXGIus/RM_1578958.MonJan131507112025 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: 1736809630 Database = /data/tmp/rModeler.cXGIus/GCA_015832495.2_NRM_Aalces_2_0.fsa - Sequences = 5939 - Bases = 2487828707 - N50 = 77421000 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124756855-133668038 | [ 1 ] 115845672-124756854 | [ ] 106934490-115845672 | [ 3 ] 98023307-106934489 | [ 2 ] 89112125-98023307 | [ 3 ] 80200942-89112124 | [ 1 ] 71289760-80200942 | [ 5 ] 62378577-71289759 | [ 2 ] 53467395-62378577 | [ 10 ] 44556212-53467394 | [ 3 ] 35645030-44556212 | [ 4 ] 26733847-35645029 | [ ] 17822665-26733847 | [ ] 8911482-17822664 | [ ] 300-8911482 |************************************************** [ 5905 ] Storage Throughput = excellent ( 1660.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41760293 bp ( 40001567 non ambiguous ) - Num Contigs Represented = 148 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:29 (hh:mm:ss) Elapsed Time Round Time: 00:10:16 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15181 repeats masked totaling 2922244 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10445038 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10035375 bp After Masking: 7091450 bp Masked: 29.34 % -- Input Database Coverage: 10445038 bp out of 2487828707 bp ( 0.42 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 39903 Comparison Time: 00:03:22 (hh:mm:ss) Elapsed Time, 5719 HSPs Collected Number of families returned by RECON: 831 Round Time: 00:04:04 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46250 repeats masked totaling 8782625 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31355175 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 30006112 bp After Masking: 21117652 bp Masked: 29.62 % -- Input Database Coverage: 41800213 bp out of 2487828707 bp ( 1.68 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 371953 Comparison Time: 00:15:43 (hh:mm:ss) Elapsed Time, 23666 HSPs Collected Number of families returned by RECON: 2386 Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149845 repeats masked totaling 29724504 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94235544 bp Num Contigs Represented = 235 Non ambiguous bp: Initial: 90003231 bp After Masking: 60038340 bp Masked: 33.29 % -- Input Database Coverage: 136035757 bp out of 2487828707 bp ( 5.47 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3211845 Comparison Time: 01:41:46 (hh:mm:ss) Elapsed Time, 91066 HSPs Collected Number of families returned by RECON: 8276 Round Time: 01:47:51 (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 : 00:05:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 488399 repeats masked totaling 96259219 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 282955416 bp Num Contigs Represented = 722 Non ambiguous bp: Initial: 270018421 bp After Masking: 172927956 bp Masked: 35.96 % -- Input Database Coverage: 418991173 bp out of 2487828707 bp ( 16.84 % ) Sampling Time: 00:14:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29656551 Comparison Time: 10:45:31 (hh:mm:ss) Elapsed Time, 178414 HSPs Collected Number of families returned by RECON: 34786 Round Time: 11:08:17 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatScout/RECON discovery complete: 840 families found Classification Time: 00:13:14 (hh:mm:ss) Elapsed Time Program Time: 13:41:13 (hh:mm:ss) Elapsed Time