RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.1qBJHp/RM_3337874.ThuNov62353342025 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: 1762502012 Database = /data/tmp/rModeler.1qBJHp/GCA_023375785.1_Penium_V1.0 - Sequences = 332786 - Bases = 3661744145 - N50 = 116173 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1359094-1456137 | [ 1 ] 1262052-1359094 | [ 3 ] 1165009-1262051 | [ 2 ] 1067967-1165009 | [ 1 ] 970924-1067966 | [ 9 ] 873882-970924 | [ 11 ] 776839-873881 | [ 19 ] 679797-776839 | [ 32 ] 582754-679796 | [ 78 ] 485712-582754 | [ 138 ] 388669-485711 | [ 308 ] 291627-388669 | [ 803 ] 194584-291626 | [ 2148 ] 97542-194584 |* [ 7214 ] 500-97542 |************************************************** [ 322019 ] Storage Throughput = excellent ( 1678.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 46560621 bp ( 40013361 non ambiguous ) - Num Contigs Represented = 4903 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 421 raw families identified - RepeatScout: Running filtering stage.. 301 families remaining - RepeatScout: 00:09:26 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 299 families... 00:15:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 66 contained, found in 00:00:09 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 00:24:50 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9028 repeats masked totaling 4597468 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11658559 bp Num Contigs Represented = 1306 Non ambiguous bp: Initial: 10015023 bp After Masking: 3483306 bp Masked: 65.22 % -- Input Database Coverage: 11658559 bp out of 3661744145 bp ( 0.32 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 853471 Comparison Time: 00:09:25 (hh:mm:ss) Elapsed Time, 49402 HSPs Collected Number of families returned by RECON: 922 Round Time: 00:13:01 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27452 repeats masked totaling 14803942 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 34903673 bp Num Contigs Represented = 3614 Non ambiguous bp: Initial: 30000029 bp After Masking: 9021951 bp Masked: 69.93 % -- Input Database Coverage: 46562232 bp out of 3661744145 bp ( 1.27 % ) Sampling Time: 00:08:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 6586635 Comparison Time: 00:26:49 (hh:mm:ss) Elapsed Time, 69560 HSPs Collected Number of families returned by RECON: 2588 Round Time: 00:37:18 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89241 repeats masked totaling 46062776 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 103921272 bp Num Contigs Represented = 10902 Non ambiguous bp: Initial: 90011569 bp After Masking: 24539925 bp Masked: 72.74 % -- Input Database Coverage: 150483504 bp out of 3661744145 bp ( 4.11 % ) Sampling Time: 00:32:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 61034676 Comparison Time: 02:00:34 (hh:mm:ss) Elapsed Time, 295371 HSPs Collected Number of families returned by RECON: 6889 Round Time: 02:37:37 (hh:mm:ss) Elapsed Time : 322 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:21:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 306104 repeats masked totaling 157384820 bp(s). - TE Masking time 00:14:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 312824010 bp Num Contigs Represented = 32536 Non ambiguous bp: Initial: 270018654 bp After Masking: 55668959 bp Masked: 79.38 % -- Input Database Coverage: 463307514 bp out of 3661744145 bp ( 12.65 % ) Sampling Time: 01:36:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 566615616 Comparison Time: 08:40:31 (hh:mm:ss) Elapsed Time, 427877 HSPs Collected Number of families returned by RECON: 19663 Round Time: 10:28:53 (hh:mm:ss) Elapsed Time : 629 families discovered. RepeatScout/RECON discovery complete: 1255 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.1qBJHp/RM_3337874.ThuNov62353342025 # 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: 00:04:40 (hh:mm:ss) Elapsed Time Program Time: 14:26:19 (hh:mm:ss) Elapsed Time