RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.tYhIDX/RM_32165.WedAug140120172024
Search Engine = rmblast 2.13.0+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1723623616
Database = /dev/shm/rModeler.tYhIDX/GCA_000340495.1_Leishmania_panamensis_L13-1.3.1   - Sequences = 952
  - Bases = 31263945
  - N50 = 158117
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  579781-621180 |                                                   [ 1 ]
  538382-579780 |                                                   [ 1 ]
  496984-538382 |                                                   [ 1 ]
  455585-496983 |                                                   [ 2 ]
  414186-455584 |                                                   [  ]
  372788-414186 |                                                   [ 1 ]
  331389-372787 |                                                   [ 5 ]
  289990-331388 |                                                   [ 3 ]
  248592-289990 |                                                   [ 11 ]
  207193-248591 |                                                   [ 12 ]
  165794-207192 |                                                   [ 15 ]
  124396-165794 |**                                                 [ 32 ]
  82997-124395  |**                                                 [ 42 ]
  41598-82996   |****                                               [ 74 ]
  200-41598     |************************************************** [ 752 ]

Storage Throughput = excellent ( 1038.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 31263900 bp ( 30965604 non ambiguous )
   - Num Contigs Represented = 952
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:56 (hh:mm:ss) Elapsed Time
Round Time: 00:17:01 (hh:mm:ss) Elapsed Time : 136 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2130 repeats masked totaling 425101 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10119310 bp
       Num Contigs Represented = 376
       Non ambiguous bp:
             Initial: 10025823 bp
             After Masking: 9572409 bp
             Masked: 4.52 % 
 -- Input Database Coverage: 10119310 bp out of 31263945 bp ( 32.37 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 116886
Comparison Time: 00:07:49 (hh:mm:ss) Elapsed Time, 3602 HSPs Collected
Number of families returned by RECON: 1101
Round Time: 00:08:23 (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 : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4725 repeats masked totaling 944373 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21144510 bp
       Num Contigs Represented = 708
       Non ambiguous bp:
             Initial: 20939701 bp
             After Masking: 19939000 bp
             Masked: 4.78 % 
 -- Input Database Coverage: 31263820 bp out of 31263945 bp ( 100.00 % )
Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 562330
Comparison Time: 00:26:24 (hh:mm:ss) Elapsed Time, 13945 HSPs Collected
Number of families returned by RECON: 3355
Round Time: 00:27:50 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 149 families found


Classification Time: 00:02:59 (hh:mm:ss) Elapsed Time


Program Time: 00:56:13 (hh:mm:ss) Elapsed Time