RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.L5FfV2/RM_252152.ThuOct220832332026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.L5FfV2/GCA_035221665.1_ASM3522166v1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1792683152 Database = /dev/shm/rModeler.L5FfV2/GCA_035221665.1_ASM3522166v1 - Sequences = 1141 - Bases = 2756528269 - N50 = 74762907 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 187703288-201110309 | [ 1 ] 174296267-187703287 | [ ] 160889247-174296267 | [ 1 ] 147482226-160889246 | [ 1 ] 134075206-147482226 | [ 1 ] 120668185-134075205 | [ 1 ] 107261164-120668184 | [ 1 ] 93854144-107261164 | [ 2 ] 80447123-93854143 | [ 2 ] 67040103-80447123 | [ 4 ] 53633082-67040102 | [ 4 ] 40226061-53633081 | [ 9 ] 26819041-40226061 | [ 8 ] 13412020-26819040 | [ 7 ] 5000-13412020 |************************************************** [ 1099 ] Storage Throughput = excellent ( 1134.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047534 bp ( 40020480 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 569 raw families identified - RepeatScout: Running filtering stage.. 513 families remaining - RepeatScout: 00:08:08 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 502 families... 00:03:09 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 198 contained, found in 00:00:07 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:08 (hh:mm:ss) Elapsed Time Round Time: 00:13:20 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26494 repeats masked totaling 6045076 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030880 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10022476 bp After Masking: 3710650 bp Masked: 62.98 % -- Input Database Coverage: 10030880 bp out of 2756528269 bp ( 0.36 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:33 (hh:mm:ss) Elapsed Time, 9229 HSPs Collected Number of families returned by RECON: 650 Round Time: 00:06:49 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 83790 repeats masked totaling 18590741 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30056654 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30038004 bp After Masking: 10665376 bp Masked: 64.49 % -- Input Database Coverage: 40087534 bp out of 2756528269 bp ( 1.45 % ) Sampling Time: 00:05:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:21:55 (hh:mm:ss) Elapsed Time, 37755 HSPs Collected Number of families returned by RECON: 1796 Round Time: 00:28:27 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 259381 repeats masked totaling 57700440 bp(s). - TE Masking time 00:04:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90101502 bp Num Contigs Represented = 146 Non ambiguous bp: Initial: 90030291 bp After Masking: 29811036 bp Masked: 66.89 % -- Input Database Coverage: 130189036 bp out of 2756528269 bp ( 4.72 % ) Sampling Time: 00:17:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 02:07:44 (hh:mm:ss) Elapsed Time, 129221 HSPs Collected Number of families returned by RECON: 4168 Round Time: 02:28:58 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 835507 repeats masked totaling 182225192 bp(s). - TE Masking time 00:21:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270235056 bp Num Contigs Represented = 287 Non ambiguous bp: Initial: 270024602 bp After Masking: 80560009 bp Masked: 70.17 % -- Input Database Coverage: 400424092 bp out of 2756528269 bp ( 14.53 % ) Sampling Time: 00:57:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 14:39:46 (hh:mm:ss) Elapsed Time, 218234 HSPs Collected Number of families returned by RECON: 11441 Round Time: 16:08:09 (hh:mm:ss) Elapsed Time : 439 families discovered. RepeatScout/RECON discovery complete: 1045 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.L5FfV2/RM_252152.ThuOct220832332026 # FamDB: # Database: Dfam # Version: 4.0 # Date: 2026-05-22 # Protein Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/PROT-Dfam_4.0/repeatpeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/CONS-Dfam_4.0/reference.fa # - 30659 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: 00:07:22 (hh:mm:ss) Elapsed Time Program Time: 19:33:05 (hh:mm:ss) Elapsed Time