RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.MZJ5K2/RM_2690877.ThuNov62347582025 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: 1762501676 Database = /dev/shm/rModeler.MZJ5K2/GCA_019843835.1_ASM1984383v1 - Sequences = 509072 - Bases = 2089776775 - N50 = 5810 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84090-90058 | [ 1 ] 78123-84090 | [ 2 ] 72156-78123 | [ 2 ] 66188-72155 | [ ] 60221-66188 | [ 3 ] 54254-60221 | [ 11 ] 48287-54254 | [ 17 ] 42319-48286 | [ 44 ] 36352-42319 | [ 103 ] 30385-36352 | [ 302 ] 24418-30385 | [ 965 ] 18450-24417 | [ 2753 ] 12483-18450 |* [ 10695 ] 6516-12483 |******** [ 72666 ] 549-6516 |************************************************** [ 421508 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = excellent ( 1679.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40188175 bp ( 40004185 non ambiguous ) - Num Contigs Represented = 9855 - 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.. : 195 raw families identified - RepeatScout: Running filtering stage.. 179 families remaining - RepeatScout: 00:01:25 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 173 families... 00:00:35 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 74 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:02:06 (hh:mm:ss) Elapsed Time : 99 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 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10770 repeats masked totaling 2019218 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10057091 bp Num Contigs Represented = 2480 Non ambiguous bp: Initial: 10000041 bp After Masking: 7779918 bp Masked: 22.20 % -- Input Database Coverage: 10057091 bp out of 2089776775 bp ( 0.48 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3073960 Comparison Time: 00:10:35 (hh:mm:ss) Elapsed Time, 52302 HSPs Collected Number of families returned by RECON: 1163 Round Time: 00:11:39 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (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... 41945 repeats masked totaling 7836577 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30131027 bp Num Contigs Represented = 7375 Non ambiguous bp: Initial: 30004087 bp After Masking: 21559684 bp Masked: 28.14 % -- Input Database Coverage: 40188118 bp out of 2089776775 bp ( 1.92 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27191625 Comparison Time: 00:37:07 (hh:mm:ss) Elapsed Time, 28513 HSPs Collected Number of families returned by RECON: 2129 Round Time: 00:38:22 (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 : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136306 repeats masked totaling 25220883 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90392049 bp Num Contigs Represented = 22019 Non ambiguous bp: Initial: 90011209 bp After Masking: 63054805 bp Masked: 29.95 % -- Input Database Coverage: 130580167 bp out of 2089776775 bp ( 6.25 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 242407171 Comparison Time: 02:39:06 (hh:mm:ss) Elapsed Time, 77805 HSPs Collected Number of families returned by RECON: 7795 Round Time: 02:43:07 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474127 repeats masked totaling 84805412 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271241243 bp Num Contigs Represented = 65730 Non ambiguous bp: Initial: 270000805 bp After Masking: 180023951 bp Masked: 33.32 % -- Input Database Coverage: 401821410 bp out of 2089776775 bp ( 19.23 % ) Sampling Time: 00:07:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2160446511 Comparison Time: 14:22:55 (hh:mm:ss) Elapsed Time, 194349 HSPs Collected Number of families returned by RECON: 33580 Round Time: 14:39:10 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 695 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.MZJ5K2/RM_2690877.ThuNov62347582025 # 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: 00:01:08 (hh:mm:ss) Elapsed Time Program Time: 18:15:33 (hh:mm:ss) Elapsed Time