RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.aAWbLA/RM_3895908.MonSep81714282025 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: 1757376868 Database = /dev/shm/rModeler.aAWbLA/GCA_002215855.1_Cryp_neof_C45_V1 - Sequences = 530 - Bases = 18184845 - N50 = 94194 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 401798-430426 | [ 1 ] 373170-401797 | [ ] 344542-373169 | [ 1 ] 315914-344541 | [ ] 287286-315913 | [ 1 ] 258658-287285 | [ ] 230030-258657 | [ 2 ] 201402-230029 | [ 6 ] 172774-201401 | [ 5 ] 144146-172773 |* [ 8 ] 115518-144145 |* [ 12 ] 86890-115517 |**** [ 32 ] 58262-86889 |**** [ 34 ] 29634-58261 |************ [ 85 ] 1007-29634 |************************************************** [ 343 ] Storage Throughput = excellent ( 1666.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 18184794 bp ( 18184784 non ambiguous ) - Num Contigs Represented = 530 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 30 raw families identified - RepeatScout: Running filtering stage.. 30 families remaining - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 27 families... 00:00:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:28 (hh:mm:ss) Elapsed Time : 22 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 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 424 repeats masked totaling 177375 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025485 bp Num Contigs Represented = 350 Non ambiguous bp: Initial: 10025485 bp After Masking: 9835013 bp Masked: 1.90 % -- Input Database Coverage: 10025485 bp out of 18184845 bp ( 55.13 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 108811 Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 2352 HSPs Collected Number of families returned by RECON: 739 Round Time: 00:04:57 (hh:mm:ss) Elapsed Time : 2 families discovered. - Increasing sample size to include end piece now = 38184845 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 38184845 bp - Sequence extraction : 00:00:00 (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... 380 repeats masked totaling 156092 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 8159229 bp Num Contigs Represented = 286 Non ambiguous bp: Initial: 8159219 bp After Masking: 7993790 bp Masked: 2.03 % -- Input Database Coverage: 18184714 bp out of 18184845 bp ( 100.00 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 66430 Comparison Time: 00:03:40 (hh:mm:ss) Elapsed Time, 1445 HSPs Collected Number of families returned by RECON: 503 Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 24 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.aAWbLA/RM_3895908.MonSep81714282025 # 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: 00:00:09 (hh:mm:ss) Elapsed Time Program Time: 00:09:25 (hh:mm:ss) Elapsed Time