RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.l3IBwD/RM_1088067.MonFeb91908302026
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: 1770692909
Database = /dev/shm/rModeler.l3IBwD/GCA_964014055.1_Leishmania_braziliensis_M2903-Dec2022 
  - Sequences = 91
  - Bases = 33495285
Storage Throughput = excellent ( 1613.23 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33495148 bp ( 33492020 non ambiguous )
   - Num Contigs Represented = 91
   - 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.. : 204 raw families identified
   - RepeatScout: Running filtering stage.. 183 families remaining
   - RepeatScout: 00:01:45 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 162 families... 00:24:52 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 34 satellite(s), 33 contained, found in 00:00:07 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:07 (hh:mm:ss) Elapsed Time
Round Time: 00:26:47 (hh:mm:ss) Elapsed Time : 96 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 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2982 repeats masked totaling 841022 bp(s).
   - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020302 bp
       Num Contigs Represented = 56
       Non ambiguous bp:
             Initial: 10019839 bp
             After Masking: 8976116 bp
             Masked: 10.42 % 
 -- Input Database Coverage: 10020302 bp out of 33495285 bp ( 29.92 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36585
Comparison Time: 00:04:07 (hh:mm:ss) Elapsed Time, 2025 HSPs Collected
Number of families returned by RECON: 696
Round Time: 00:04:41 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6543 repeats masked totaling 1878195 bp(s).
   - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23474822 bp
       Num Contigs Represented = 71
       Non ambiguous bp:
             Initial: 23472157 bp
             After Masking: 21107314 bp
             Masked: 10.08 % 
 -- Input Database Coverage: 33495124 bp out of 33495285 bp ( 100.00 % )
Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 190653
Comparison Time: 00:13:48 (hh:mm:ss) Elapsed Time, 12111 HSPs Collected
Number of families returned by RECON: 2641
Round Time: 00:22:50 (hh:mm:ss) Elapsed Time : 16 families discovered.

RepeatScout/RECON discovery complete: 114 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.l3IBwD/RM_1088067.MonFeb91908302026
# 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: 00:00:30 (hh:mm:ss) Elapsed Time


Program Time: 00:54:48 (hh:mm:ss) Elapsed Time