RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.pPzFkM/RM_401012.ThuSep41214222025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1757013261 Database = /dev/shm/rModeler.pPzFkM/GCA_011100555.2_mCalJa1.2.pat.X - Sequences = 1234 - Bases = 2874881015 - N50 = 146897247 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202510801-216975769 | [ 2 ] 188045833-202510800 | [ 1 ] 173580866-188045833 | [ ] 159115898-173580865 | [ 3 ] 144650930-159115897 | [ 2 ] 130185963-144650930 | [ 2 ] 115720995-130185962 | [ 4 ] 101256027-115720994 | [ 1 ] 86791060-101256027 | [ 2 ] 72326092-86791059 | [ 1 ] 57861124-72326091 | [ ] 43396157-57861124 | [ 5 ] 28931189-43396156 | [ ] 14466221-28931188 | [ ] 1254-14466221 |************************************************** [ 1211 ] Storage Throughput = excellent ( 1177.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40168393 bp ( 40028763 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 178 raw families identified - RepeatScout: Running filtering stage.. 165 families remaining - RepeatScout: 00:03:52 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 160 families... 00:04:11 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 74 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:10:44 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18444 repeats masked totaling 2983697 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001103 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001090 bp After Masking: 6880608 bp Masked: 31.20 % -- Input Database Coverage: 10001103 bp out of 2874881015 bp ( 0.35 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 10048 HSPs Collected Number of families returned by RECON: 966 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49575 repeats masked totaling 10327423 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30167210 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30027593 bp After Masking: 18836458 bp Masked: 37.27 % -- Input Database Coverage: 40168313 bp out of 2874881015 bp ( 1.40 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:29:11 (hh:mm:ss) Elapsed Time, 29967 HSPs Collected Number of families returned by RECON: 1891 Round Time: 00:34:38 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162624 repeats masked totaling 34489222 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90418905 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90002011 bp After Masking: 53468418 bp Masked: 40.59 % -- Input Database Coverage: 130587218 bp out of 2874881015 bp ( 4.54 % ) Sampling Time: 00:12:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 03:15:50 (hh:mm:ss) Elapsed Time, 73597 HSPs Collected Number of families returned by RECON: 6104 Round Time: 03:31:41 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 527351 repeats masked totaling 110785001 bp(s). - TE Masking time 00:07:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271922298 bp Num Contigs Represented = 237 Non ambiguous bp: Initial: 270019498 bp After Masking: 153281858 bp Masked: 43.23 % -- Input Database Coverage: 402509516 bp out of 2874881015 bp ( 14.00 % ) Sampling Time: 00:39:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23560680 Comparison Time: 25:03:52 (hh:mm:ss) Elapsed Time, 215843 HSPs Collected Number of families returned by RECON: 25007 Round Time: 25:59:54 (hh:mm:ss) Elapsed Time : 321 families discovered. RepeatScout/RECON discovery complete: 651 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.pPzFkM/RM_401012.ThuSep41214222025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:03:58 (hh:mm:ss) Elapsed Time Program Time: 30:28:19 (hh:mm:ss) Elapsed Time