RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Y4loYD/RM_3965940.MonSep81253552025 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: 1757361234 Database = /dev/shm/rModeler.Y4loYD/GCA_000836315.1_Cryp_gatt_LA55_V1 - Sequences = 134 - Bases = 17360036 - N50 = 445652 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 962577-1031261 |* [ 2 ] 893893-962576 | [ 1 ] 825209-893892 | [ ] 756525-825208 | [ 1 ] 687841-756524 | [ 1 ] 619157-687840 | [ ] 550473-619156 |** [ 4 ] 481789-550472 | [ 1 ] 413105-481788 |* [ 3 ] 344421-413104 |* [ 3 ] 275737-344420 |** [ 4 ] 207053-275736 |**** [ 7 ] 138369-207052 |******** [ 13 ] 69685-138368 |******** [ 14 ] 1002-69685 |************************************************** [ 80 ] Storage Throughput = excellent ( 1647.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 17359957 bp ( 17329897 non ambiguous ) - Num Contigs Represented = 134 - 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.. : 11 raw families identified - RepeatScout: Running filtering stage.. 10 families remaining - RepeatScout: 00:00:14 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 10 families... 00:00:04 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:21 (hh:mm:ss) Elapsed Time : 10 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... 213 repeats masked totaling 45187 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026845 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 10012170 bp After Masking: 9956478 bp Masked: 0.56 % -- Input Database Coverage: 10026845 bp out of 17360036 bp ( 57.76 % ) Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 44551 Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 1498 HSPs Collected Number of families returned by RECON: 593 Round Time: 00:04:10 (hh:mm:ss) Elapsed Time : 1 families discovered. - Increasing sample size to include end piece now = 37360036 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 37360036 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181 repeats masked totaling 39375 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 7333032 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 7317647 bp After Masking: 7270398 bp Masked: 0.65 % -- Input Database Coverage: 17359877 bp out of 17360036 bp ( 100.00 % ) Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24310 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 827 HSPs Collected Number of families returned by RECON: 357 Round Time: 00:02:58 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 11 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Y4loYD/RM_3965940.MonSep81253552025 # 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: 00:00:05 (hh:mm:ss) Elapsed Time Program Time: 00:07:34 (hh:mm:ss) Elapsed Time