RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.nPY1Wd/RM_631067.MonSep82040302025 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: 1757389229 Database = /data/tmp/rModeler.nPY1Wd/GCA_003521245.1_ASM352124v1 - Sequences = 11961 - Bases = 51778905 - N50 = 14998 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 143478-153713 | [ 2 ] 133244-143478 | [ ] 123010-133244 | [ 2 ] 112776-123010 | [ 3 ] 102542-112776 | [ 4 ] 92307-102541 | [ 3 ] 82073-92307 | [ 6 ] 71839-82073 | [ 13 ] 61605-71839 | [ 20 ] 51371-61605 | [ 40 ] 41136-51370 | [ 50 ] 30902-41136 | [ 107 ] 20668-30902 |* [ 310 ] 10434-20668 |*** [ 769 ] 200-10434 |************************************************** [ 10632 ] Storage Throughput = good ( 860.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40112661 bp ( 40001711 non ambiguous ) - Num Contigs Represented = 9367 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 369 raw families identified - RepeatScout: Running filtering stage.. 359 families remaining - RepeatScout: 00:02:13 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 345 families... 00:02:40 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 78 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 00:05:09 (hh:mm:ss) Elapsed Time : 267 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 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3357 repeats masked totaling 1709992 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10054251 bp Num Contigs Represented = 2428 Non ambiguous bp: Initial: 10026608 bp After Masking: 8275626 bp Masked: 17.46 % -- Input Database Coverage: 10054251 bp out of 51778905 bp ( 19.42 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2963395 Comparison Time: 00:14:40 (hh:mm:ss) Elapsed Time, 7094 HSPs Collected Number of families returned by RECON: 1511 Round Time: 00:16:06 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9865 repeats masked totaling 4948690 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30083661 bp Num Contigs Represented = 6972 Non ambiguous bp: Initial: 30000334 bp After Masking: 24936981 bp Masked: 16.88 % -- Input Database Coverage: 40137912 bp out of 51778905 bp ( 77.52 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24713965 Comparison Time: 00:54:07 (hh:mm:ss) Elapsed Time, 36828 HSPs Collected Number of families returned by RECON: 6465 Round Time: 01:00:28 (hh:mm:ss) Elapsed Time : 26 families discovered. - Increasing sample size to include end piece now = 101724654 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 101724654 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3941 repeats masked totaling 2121196 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11640834 bp Num Contigs Represented = 2656 Non ambiguous bp: Initial: 11613727 bp After Masking: 9440368 bp Masked: 18.71 % -- Input Database Coverage: 51778746 bp out of 51778905 bp ( 100.00 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3571128 Comparison Time: 00:19:36 (hh:mm:ss) Elapsed Time, 4917 HSPs Collected Number of families returned by RECON: 1689 Round Time: 00:21:00 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 301 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.nPY1Wd/RM_631067.MonSep82040302025 # 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: 00:02:30 (hh:mm:ss) Elapsed Time Program Time: 01:45:13 (hh:mm:ss) Elapsed Time