RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.c32r8a/RM_28521.TueJul161410492024 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: 1721164243 Database = /dev/shm/rModeler.c32r8a/GCF_010015445.1_GENO_Pfluv_1.0 - Sequences = 303 - Bases = 951345774 - N50 = 40300294 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 45475907-48724115 | [ 3 ] 42227699-45475906 | [ 4 ] 38979491-42227698 |* [ 7 ] 35731283-38979490 |* [ 6 ] 32483075-35731282 | [ 1 ] 29234867-32483074 | [ 1 ] 25986659-29234866 | [ 1 ] 22738452-25986659 | [ ] 19490244-22738451 | [ 1 ] 16242036-19490243 | [ ] 12993828-16242035 | [ ] 9745620-12993827 | [ ] 6497412-9745619 | [ ] 3249204-6497411 | [ ] 997-3249204 |************************************************** [ 279 ] Storage Throughput = excellent ( 1119.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038504 bp ( 40025610 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:41 (hh:mm:ss) Elapsed Time Round Time: 00:44:55 (hh:mm:ss) Elapsed Time : 1178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15218 repeats masked totaling 2859414 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027399 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10024639 bp After Masking: 6478459 bp Masked: 35.37 % -- Input Database Coverage: 10027399 bp out of 951345774 bp ( 1.05 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:25:49 (hh:mm:ss) Elapsed Time, 8365 HSPs Collected Number of families returned by RECON: 1668 Round Time: 00:28:48 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45727 repeats masked totaling 8168429 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011086 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30000952 bp After Masking: 19958930 bp Masked: 33.47 % -- Input Database Coverage: 40038485 bp out of 951345774 bp ( 4.21 % ) Sampling Time: 00:05:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 01:46:17 (hh:mm:ss) Elapsed Time, 50956 HSPs Collected Number of families returned by RECON: 5583 Round Time: 01:56:36 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142893 repeats masked totaling 25482792 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90062806 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90038474 bp After Masking: 58898136 bp Masked: 34.59 % -- Input Database Coverage: 130101291 bp out of 951345774 bp ( 13.68 % ) Sampling Time: 00:17:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 07:27:53 (hh:mm:ss) Elapsed Time, 336968 HSPs Collected Number of families returned by RECON: 16590 Round Time: 08:19:44 (hh:mm:ss) Elapsed Time : 739 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 512185 repeats masked totaling 93402963 bp(s). - TE Masking time 00:18:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270115799 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270034265 bp After Masking: 160590390 bp Masked: 40.53 % -- Input Database Coverage: 400217090 bp out of 951345774 bp ( 42.07 % ) Sampling Time: 00:56:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23266431 Comparison Time: 46:47:09 (hh:mm:ss) Elapsed Time, 941659 HSPs Collected Number of families returned by RECON: 52046 Round Time: 49:55:04 (hh:mm:ss) Elapsed Time : 1696 families discovered. RepeatScout/RECON discovery complete: 3752 families found Classification Time: 02:35:21 (hh:mm:ss) Elapsed Time Program Time: 64:00:28 (hh:mm:ss) Elapsed Time