RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.NfLAXK/RM_1826392.SunNov172020572024 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: 1731903656 Database = /scratch/tmp/rModeler.NfLAXK/GCA_964237555.1_mOryCun1.1 - Sequences = 222 - Bases = 2804674863 - N50 = 164456403 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 222327774-238208258 | [ 1 ] 206447290-222327773 | [ ] 190566806-206447289 | [ 1 ] 174686322-190566805 | [ 2 ] 158805838-174686321 | [ 3 ] 142925354-158805837 | [ 1 ] 127044870-142925353 | [ 2 ] 111164387-127044870 | [ 3 ] 95283903-111164386 | [ 2 ] 79403419-95283902 | [ 1 ] 63522935-79403418 |* [ 4 ] 47642451-63522934 | [ 1 ] 31761967-47642450 | [ 1 ] 15881483-31761966 | [ ] 1000-15881483 |************************************************** [ 200 ] Storage Throughput = excellent ( 1571.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034787 bp ( 40027498 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:46 (hh:mm:ss) Elapsed Time Round Time: 00:12:46 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16527 repeats masked totaling 4001277 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005879 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10004079 bp After Masking: 5762976 bp Masked: 42.39 % -- Input Database Coverage: 10005879 bp out of 2804674863 bp ( 0.36 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:37 (hh:mm:ss) Elapsed Time, 4320 HSPs Collected Number of families returned by RECON: 586 Round Time: 00:03:35 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50943 repeats masked totaling 11753556 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028828 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30023339 bp After Masking: 17805052 bp Masked: 40.70 % -- Input Database Coverage: 40034707 bp out of 2804674863 bp ( 1.43 % ) Sampling Time: 00:02:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:10:52 (hh:mm:ss) Elapsed Time, 17392 HSPs Collected Number of families returned by RECON: 1822 Round Time: 00:13:20 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 161975 repeats masked totaling 36779101 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019020 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90004420 bp After Masking: 51346836 bp Masked: 42.95 % -- Input Database Coverage: 130053727 bp out of 2804674863 bp ( 4.64 % ) Sampling Time: 00:06:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:00:40 (hh:mm:ss) Elapsed Time, 65956 HSPs Collected Number of families returned by RECON: 6845 Round Time: 01:08:33 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 508718 repeats masked totaling 115446897 bp(s). - TE Masking time 00:03:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270078893 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 270035089 bp After Masking: 149234317 bp Masked: 44.74 % -- Input Database Coverage: 400132620 bp out of 2804674863 bp ( 14.27 % ) Sampling Time: 00:19:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 07:05:14 (hh:mm:ss) Elapsed Time, 255115 HSPs Collected Number of families returned by RECON: 28681 Round Time: 07:35:26 (hh:mm:ss) Elapsed Time : 372 families discovered. RepeatScout/RECON discovery complete: 731 families found Classification Time: 00:17:16 (hh:mm:ss) Elapsed Time Program Time: 09:30:56 (hh:mm:ss) Elapsed Time