RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.imKJOe/RM_1307306.WedSep100711352025 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: 1757513495 Database = /dev/shm/rModeler.imKJOe/GCA_014898885.1_ASM1489888v1 - Sequences = 1502 - Bases = 43920991 - N50 = 74134 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 414317-443876 | [ 1 ] 384759-414317 | [ ] 355201-384759 | [ ] 325643-355201 | [ 1 ] 296085-325643 | [ ] 266527-296085 | [ 3 ] 236969-266527 | [ 2 ] 207411-236969 | [ 6 ] 177853-207411 | [ 8 ] 148295-177853 |* [ 21 ] 118737-148295 |** [ 42 ] 89179-118737 |** [ 47 ] 59621-89179 |**** [ 103 ] 30063-59621 |********** [ 218 ] 505-30063 |************************************************** [ 1050 ] Storage Throughput = excellent ( 1645.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030090 bp ( 40028725 non ambiguous ) - Num Contigs Represented = 1403 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 16 raw families identified - RepeatScout: Running filtering stage.. 15 families remaining - RepeatScout: 00:00:42 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 15 families... 00:00:06 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:52 (hh:mm:ss) Elapsed Time : 12 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 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 312 repeats masked totaling 51725 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004193 bp Num Contigs Represented = 430 Non ambiguous bp: Initial: 10003946 bp After Masking: 9943526 bp Masked: 0.60 % -- Input Database Coverage: 10004193 bp out of 43920991 bp ( 22.78 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 116403 Comparison Time: 00:04:46 (hh:mm:ss) Elapsed Time, 2331 HSPs Collected Number of families returned by RECON: 676 Round Time: 00:04:56 (hh:mm:ss) Elapsed Time : 2 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 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1123 repeats masked totaling 160382 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025866 bp Num Contigs Represented = 1147 Non ambiguous bp: Initial: 30024748 bp After Masking: 29837623 bp Masked: 0.62 % -- Input Database Coverage: 40030059 bp out of 43920991 bp ( 91.14 % ) Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1101870 Comparison Time: 00:18:34 (hh:mm:ss) Elapsed Time, 14821 HSPs Collected Number of families returned by RECON: 3779 Round Time: 00:19:08 (hh:mm:ss) Elapsed Time : 16 families discovered. - Increasing sample size to include end piece now = 93916798 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 93916798 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... 155 repeats masked totaling 21123 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3890852 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 3890701 bp After Masking: 3866051 bp Masked: 0.63 % -- Input Database Coverage: 43920911 bp out of 43920991 bp ( 100.00 % ) Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17766 Comparison Time: 00:01:37 (hh:mm:ss) Elapsed Time, 169 HSPs Collected Number of families returned by RECON: 118 Round Time: 00:01:41 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 30 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.imKJOe/RM_1307306.WedSep100711352025 # 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: 00:00:07 (hh:mm:ss) Elapsed Time Program Time: 00:26:44 (hh:mm:ss) Elapsed Time