RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UY6XTl/RM_1557550.TueJan91152292024 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: 1704829946 Database = /dev/shm/rModeler.UY6XTl/GCF_902713615.1_sScyCan1.1 - Sequences = 646 - Bases = 4220406627 - N50 = 199962141 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 292663682-313568160 | [ 1 ] 271759204-292663681 | [ 2 ] 250854727-271759204 | [ ] 229950249-250854726 | [ 2 ] 209045771-229950248 | [ 2 ] 188141294-209045771 | [ 3 ] 167236816-188141293 | [ 1 ] 146332338-167236815 | [ 4 ] 125427861-146332338 | [ 3 ] 104523383-125427860 | [ 1 ] 83618905-104523382 | [ 1 ] 62714428-83618905 | [ 1 ] 41809950-62714427 | [ ] 20905472-41809949 | [ 6 ] 995-20905472 |************************************************** [ 619 ] Storage Throughput = excellent ( 1320.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40678027 bp ( 40027913 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:02 (hh:mm:ss) Elapsed Time Round Time: 00:25:11 (hh:mm:ss) Elapsed Time : 727 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21657 repeats masked totaling 5778293 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10158617 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10013840 bp After Masking: 3758419 bp Masked: 62.47 % -- Input Database Coverage: 10158617 bp out of 4220406627 bp ( 0.24 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 8659 HSPs Collected Number of families returned by RECON: 1092 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67331 repeats masked totaling 17885322 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30519330 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30013993 bp After Masking: 10437427 bp Masked: 65.22 % -- Input Database Coverage: 40677947 bp out of 4220406627 bp ( 0.96 % ) Sampling Time: 00:07:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:20:36 (hh:mm:ss) Elapsed Time, 40009 HSPs Collected Number of families returned by RECON: 2843 Round Time: 00:30:01 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214359 repeats masked totaling 56508648 bp(s). - TE Masking time 00:02:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91493563 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90025441 bp After Masking: 29027262 bp Masked: 67.76 % -- Input Database Coverage: 132171510 bp out of 4220406627 bp ( 3.13 % ) Sampling Time: 00:22:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2636956 Comparison Time: 01:45:52 (hh:mm:ss) Elapsed Time, 151026 HSPs Collected Number of families returned by RECON: 7705 Round Time: 02:13:49 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 697167 repeats masked totaling 179752476 bp(s). - TE Masking time 00:09:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274020396 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 270038964 bp After Masking: 75605913 bp Masked: 72.00 % -- Input Database Coverage: 406191906 bp out of 4220406627 bp ( 9.62 % ) Sampling Time: 01:11:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23560680 Comparison Time: 10:22:33 (hh:mm:ss) Elapsed Time, 388496 HSPs Collected Number of families returned by RECON: 19552 Round Time: 11:50:35 (hh:mm:ss) Elapsed Time : 775 families discovered. RepeatScout/RECON discovery complete: 2017 families found Classification Time: 00:56:58 (hh:mm:ss) Elapsed Time Program Time: 16:04:26 (hh:mm:ss) Elapsed Time