RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.E2NYaa/RM_3745933.SunSep130942392026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.E2NYaa/GCA_056824615.1_fAleTen1.hap2, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1789317758 Database = /dev/shm/rModeler.E2NYaa/GCA_056824615.1_fAleTen1.hap2 - Sequences = 1461 - Bases = 2098279840 - N50 = 176197888 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 178868652-191644269 | [ 4 ] 166093035-178868651 | [ 3 ] 153317418-166093034 | [ ] 140541801-153317417 | [ 1 ] 127766184-140541800 | [ 2 ] 114990567-127766183 | [ 1 ] 102214950-114990566 | [ ] 89439333-102214949 | [ ] 76663716-89439332 | [ ] 63888099-76663715 | [ ] 51112482-63888098 | [ 2 ] 38336865-51112481 | [ ] 25561248-38336864 | [ ] 12785631-25561247 | [ ] 10015-12785631 |************************************************** [ 1448 ] Storage Throughput = excellent ( 1873.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033402 bp ( 40012343 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 1415 raw families identified - RepeatScout: Running filtering stage.. 1353 families remaining - RepeatScout: 00:03:48 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 1311 families... 03:43:50 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 26 satellite(s), 421 contained, found in 00:00:11 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:11 (hh:mm:ss) Elapsed Time Round Time: 03:49:01 (hh:mm:ss) Elapsed Time : 863 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15734 repeats masked totaling 4293005 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036128 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10031128 bp After Masking: 5053668 bp Masked: 49.62 % -- Input Database Coverage: 10036128 bp out of 2098279840 bp ( 0.48 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:36 (hh:mm:ss) Elapsed Time, 39535 HSPs Collected Number of families returned by RECON: 2060 Round Time: 00:05:07 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50774 repeats masked totaling 13747523 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037274 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30021215 bp After Masking: 14732947 bp Masked: 50.92 % -- Input Database Coverage: 40073402 bp out of 2098279840 bp ( 1.91 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:14:13 (hh:mm:ss) Elapsed Time, 220369 HSPs Collected Number of families returned by RECON: 5845 Round Time: 00:18:25 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 171654 repeats masked totaling 45327935 bp(s). - TE Masking time 00:02:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047433 bp Num Contigs Represented = 205 Non ambiguous bp: Initial: 90001232 bp After Masking: 39541510 bp Masked: 56.07 % -- Input Database Coverage: 130120835 bp out of 2098279840 bp ( 6.20 % ) Sampling Time: 00:10:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 01:06:53 (hh:mm:ss) Elapsed Time, 580681 HSPs Collected Number of families returned by RECON: 13904 Round Time: 01:25:07 (hh:mm:ss) Elapsed Time : 871 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 624844 repeats masked totaling 162709395 bp(s). - TE Masking time 00:17:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270163026 bp Num Contigs Represented = 431 Non ambiguous bp: Initial: 270011805 bp After Masking: 92464427 bp Masked: 65.76 % -- Input Database Coverage: 400283861 bp out of 2098279840 bp ( 19.08 % ) Sampling Time: 00:37:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23382541 Comparison Time: 05:58:01 (hh:mm:ss) Elapsed Time, 1281034 HSPs Collected Number of families returned by RECON: 28725 Round Time: 06:59:59 (hh:mm:ss) Elapsed Time : 1610 families discovered. RepeatScout/RECON discovery complete: 3556 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.E2NYaa/RM_3745933.SunSep130942392026 # 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: 00:08:39 (hh:mm:ss) Elapsed Time Program Time: 12:46:18 (hh:mm:ss) Elapsed Time