RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Hr3JyY/RM_417137.MonSep81350012025 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: 1757364600 Database = /dev/shm/rModeler.Hr3JyY/GCA_001466635.1_ASM146663v1 - Sequences = 194 - Bases = 14533275 - N50 = 183086 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 546428-585387 | [ 1 ] 507469-546427 | [ 2 ] 468510-507468 | [ 1 ] 429551-468509 | [ 1 ] 390592-429550 | [ 2 ] 351633-390591 | [ 1 ] 312674-351632 | [ 2 ] 273716-312674 | [ 1 ] 234757-273715 |* [ 4 ] 195798-234756 | [ 2 ] 156839-195797 |** [ 6 ] 117880-156838 |****** [ 14 ] 78921-117879 |*********** [ 23 ] 39962-78920 |*************** [ 31 ] 1004-39962 |************************************************** [ 103 ] Storage Throughput = excellent ( 1662.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14533207 bp ( 14506941 non ambiguous ) - Num Contigs Represented = 194 - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 33 raw families identified - RepeatScout: Running filtering stage.. 32 families remaining - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 24 families... 00:00:05 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:33 (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 : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 306 repeats masked totaling 77533 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10054032 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 10036616 bp After Masking: 9875668 bp Masked: 1.60 % -- Input Database Coverage: 10054032 bp out of 14533275 bp ( 69.18 % ) Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 56616 Comparison Time: 00:04:28 (hh:mm:ss) Elapsed Time, 3042 HSPs Collected Number of families returned by RECON: 659 Round Time: 00:04:40 (hh:mm:ss) Elapsed Time : 0 families discovered. - Increasing sample size to include end piece now = 34533275 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34533275 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... 134 repeats masked totaling 26571 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4479095 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 4470245 bp After Masking: 4418187 bp Masked: 1.16 % -- Input Database Coverage: 14533127 bp out of 14533275 bp ( 100.00 % ) Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 10011 Comparison Time: 00:01:39 (hh:mm:ss) Elapsed Time, 572 HSPs Collected Number of families returned by RECON: 241 Round Time: 00:01:44 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 22 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Hr3JyY/RM_417137.MonSep81350012025 # 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: 00:00:06 (hh:mm:ss) Elapsed Time Program Time: 00:07:03 (hh:mm:ss) Elapsed Time