RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3AwSpy/RM_17992.TueDec51429172023 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: 1701815356 Database = /dev/shm/rModeler.3AwSpy/GCA_902713615.2_sScyCan1.2 - Sequences = 645 - Bases = 4220389930 - 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 |************************************************** [ 618 ] Storage Throughput = excellent ( 1157.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40863275 bp ( 40019349 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:06 (hh:mm:ss) Elapsed Time Round Time: 00:32:56 (hh:mm:ss) Elapsed Time : 734 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21220 repeats masked totaling 5886065 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10122307 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10020679 bp After Masking: 3631082 bp Masked: 63.76 % -- Input Database Coverage: 10122307 bp out of 4220389930 bp ( 0.24 % ) Sampling Time: 00:02:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:55 (hh:mm:ss) Elapsed Time, 6455 HSPs Collected Number of families returned by RECON: 1037 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66179 repeats masked totaling 17904928 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30780810 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30038512 bp After Masking: 10600828 bp Masked: 64.71 % -- Input Database Coverage: 40903117 bp out of 4220389930 bp ( 0.97 % ) Sampling Time: 00:08:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 298378 Comparison Time: 00:20:54 (hh:mm:ss) Elapsed Time, 47414 HSPs Collected Number of families returned by RECON: 2943 Round Time: 00:31:05 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 210886 repeats masked totaling 56268932 bp(s). - TE Masking time 00:03:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91569392 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90007864 bp After Masking: 28621088 bp Masked: 68.20 % -- Input Database Coverage: 132472509 bp out of 4220389930 bp ( 3.14 % ) Sampling Time: 00:26:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2641551 Comparison Time: 01:58:38 (hh:mm:ss) Elapsed Time, 165634 HSPs Collected Number of families returned by RECON: 7641 Round Time: 02:32:04 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 680808 repeats masked totaling 180398112 bp(s). - TE Masking time 00:14:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274263708 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 270001102 bp After Masking: 75206255 bp Masked: 72.15 % -- Input Database Coverage: 406736217 bp out of 4220389930 bp ( 9.64 % ) Sampling Time: 01:20:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23684403 Comparison Time: 13:14:25 (hh:mm:ss) Elapsed Time, 409876 HSPs Collected Number of families returned by RECON: 19598 Round Time: 15:02:14 (hh:mm:ss) Elapsed Time : 846 families discovered. RepeatScout/RECON discovery complete: 2076 families found Classification Time: 01:14:42 (hh:mm:ss) Elapsed Time Program Time: 20:00:50 (hh:mm:ss) Elapsed Time