RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.qWDcCf/RM_3515160.ThuSep41257272025 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: 1757015846 Database = /dev/shm/rModeler.qWDcCf/GCA_044231685.1_ASM4423168v1 - Sequences = 355 - Bases = 500467214 - N50 = 23515437 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33940250-36364483 | [ 1 ] 31516018-33940250 | [ 2 ] 29091786-31516018 | [ 2 ] 26667554-29091786 | [ ] 24243322-26667554 | [ 2 ] 21819089-24243321 | [ 5 ] 19394857-21819089 | [ 2 ] 16970625-19394857 | [ 2 ] 14546393-16970625 | [ 4 ] 12122161-14546393 | [ ] 9697928-12122160 | [ ] 7273696-9697928 | [ ] 4849464-7273696 | [ ] 2425232-4849464 | [ ] 1000-2425232 |************************************************** [ 335 ] Storage Throughput = excellent ( 1695.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025239 bp ( 40024339 non ambiguous ) - Num Contigs Represented = 71 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 278 raw families identified - RepeatScout: Running filtering stage.. 247 families remaining - RepeatScout: 00:02:40 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 233 families... 00:00:33 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 95 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:03:28 (hh:mm:ss) Elapsed Time : 133 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 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3907 repeats masked totaling 762681 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023098 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10022998 bp After Masking: 8788942 bp Masked: 12.31 % -- Input Database Coverage: 10023098 bp out of 500467214 bp ( 2.00 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:43 (hh:mm:ss) Elapsed Time, 17614 HSPs Collected Number of families returned by RECON: 1223 Round Time: 00:05:23 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16291 repeats masked totaling 3099111 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002061 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30001261 bp After Masking: 24852468 bp Masked: 17.16 % -- Input Database Coverage: 40025159 bp out of 500467214 bp ( 8.00 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:15:15 (hh:mm:ss) Elapsed Time, 44413 HSPs Collected Number of families returned by RECON: 4062 Round Time: 00:20:40 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60601 repeats masked totaling 10858005 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007657 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 90005157 bp After Masking: 72120562 bp Masked: 19.87 % -- Input Database Coverage: 130032816 bp out of 500467214 bp ( 25.98 % ) Sampling Time: 00:20:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 01:34:53 (hh:mm:ss) Elapsed Time, 204035 HSPs Collected Number of families returned by RECON: 14302 Round Time: 01:59:25 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 244748 repeats masked totaling 41799326 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020061 bp Num Contigs Represented = 256 Non ambiguous bp: Initial: 270013761 bp After Masking: 209428683 bp Masked: 22.44 % -- Input Database Coverage: 400052877 bp out of 500467214 bp ( 79.94 % ) Sampling Time: 00:55:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23444128 Comparison Time: 11:12:04 (hh:mm:ss) Elapsed Time, 535387 HSPs Collected Number of families returned by RECON: 57323 Round Time: 12:37:19 (hh:mm:ss) Elapsed Time : 635 families discovered. RepeatScout/RECON discovery complete: 1118 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.qWDcCf/RM_3515160.ThuSep41257272025 # 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: 00:02:21 (hh:mm:ss) Elapsed Time Program Time: 15:08:36 (hh:mm:ss) Elapsed Time