RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.42a9xe/RM_1709231.MonSep82025022025 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: 1757388301 Database = /dev/shm/rModeler.42a9xe/GCA_003316975.2_ASM331697v2 - Sequences = 255 - Bases = 42535067 - N50 = 4098502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 5725652-6134554 | [ 1 ] 5316750-5725651 | [ ] 4907849-5316750 | [ ] 4498947-4907848 | [ 1 ] 4090046-4498947 | [ 2 ] 3681144-4090045 | [ 2 ] 3272242-3681143 | [ ] 2863341-3272242 | [ ] 2454439-2863340 | [ 2 ] 2045538-2454439 | [ 2 ] 1636636-2045537 | [ ] 1227734-1636635 | [ 1 ] 818833-1227734 | [ ] 409931-818832 | [ ] 1030-409931 |************************************************** [ 244 ] Storage Throughput = excellent ( 1682.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40105851 bp ( 40029451 non ambiguous ) - Num Contigs Represented = 248 - 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.. : 48 raw families identified - RepeatScout: Running filtering stage.. 28 families remaining - RepeatScout: 00:00:44 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 27 families... 00:02:03 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 4 contained, found in 00:00:07 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:07 (hh:mm:ss) Elapsed Time Round Time: 00:02:59 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 514 repeats masked totaling 136896 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021273 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 10002373 bp After Masking: 9854990 bp Masked: 1.47 % -- Input Database Coverage: 10021273 bp out of 42535067 bp ( 23.56 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 46360 Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 1745 HSPs Collected Number of families returned by RECON: 604 Round Time: 00:13:25 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1637 repeats masked totaling 398213 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30084530 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 30027030 bp After Masking: 29598068 bp Masked: 1.43 % -- Input Database Coverage: 40105803 bp out of 42535067 bp ( 94.29 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 412686 Comparison Time: 00:19:37 (hh:mm:ss) Elapsed Time, 14622 HSPs Collected Number of families returned by RECON: 3231 Round Time: 01:08:38 (hh:mm:ss) Elapsed Time : 12 families discovered. - Increasing sample size to include end piece now = 92513794 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 92513794 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177 repeats masked totaling 44795 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2429101 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 2425001 bp After Masking: 2377673 bp Masked: 1.95 % -- Input Database Coverage: 42534904 bp out of 42535067 bp ( 100.00 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2278 Comparison Time: 00:00:46 (hh:mm:ss) Elapsed Time, 60 HSPs Collected Number of families returned by RECON: 50 Round Time: 00:01:18 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 36 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.42a9xe/RM_1709231.MonSep82025022025 # 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: 00:00:16 (hh:mm:ss) Elapsed Time Program Time: 01:26:36 (hh:mm:ss) Elapsed Time