Example command: 
For third-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 17 KmerCovTh 2 MinOverlap 20 AdaptiveTh 0.005 f reads_file1.fq/fa f reads_file2.fq/fa
For sec-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 31 KmerCovTh 0 MinOverlap 50 PathCovTh 1 f reads_file1.fq/fa f reads_file2.fq/fa
Parameters:
MinLen: min read length for a read to be used.
Contigs:  contig file to be used.
k: k-mer size.
LD: load compressed reads information. You can set to 1 if you have run the algorithm for one round and just want to fine tune the following parameters.
PARAMETERS THAT ARE CRITICAL FOR THE PERFORMANCE:
If you have high coverage, set large values to these parameters.
KmerCovTh: k-mer matching threshold for each solid contig. (suggest 2-10)
MinOverlap: min matching k-mers for each two reads. (suggest 10-150)
AdaptiveTh: [Specific for third-gen sequencing] adaptive k-mer threshold for each solid contig. (suggest 0.001-0.02)
PathCovTh: [Specific for Illumina sequencing] occurence threshold for a compressed read. (suggest 1-3)
Author: Chengxi Ye cxy@umd.edu.
last update: Jun 11, 2015.
Loading contigs.
1459770087 k-mers in round 1.
916262275 k-mers in round 2.
Analyzing reads...
File1: /work/RokhsarU/daria/dr_lab_stuff/pb/subreads/cat_all_subreads_over_2000.fa
Long reads indexed. 
Total Kmers: 159633193573
Matching Unique Kmers: 24273735245
Compression time: 76924 secs.
Scoring method: 3
Match method: 2
Loading long read index
Loading file: ReadsInfoFrom_cat_all_subreads_over_2000.fa
7031049 reads loaded.
Average size: 9
Loaded.
7031049 reads.
Calculating reads overlaps, round 1
Multiple alignment for error correction.
1000000 sequences aligned.
Avg alignment size: 11
total alignments: 28700230
2000000 sequences aligned.
Avg alignment size: 11
total alignments: 61150785
3000000 sequences aligned.
Avg alignment size: 12
total alignments: 97594784
4000000 sequences aligned.
Avg alignment size: 12
total alignments: 130756645
5000000 sequences aligned.
Avg alignment size: 12
total alignments: 169487469
6000000 sequences aligned.
Avg alignment size: 12
total alignments: 203974355
7000000 sequences aligned.
Avg alignment size: 12
total alignments: 244445472
Avg alignment size: 12
Avg sparse alignment size: 4
total alignments: 245762355
Loading file: CleanedLongReads.txt
6444911 reads loaded.
Average size: 8
Done.
MSA time: 5564 secs.
1000000 reads aligned.
Avg alignment size: 11
total alignments: 6071471
2000000 reads aligned.
Avg alignment size: 12
total alignments: 10666337
3000000 reads aligned.
Avg alignment size: 12
total alignments: 13887780
4000000 reads aligned.
Avg alignment size: 12
total alignments: 16873971
5000000 reads aligned.
Avg alignment size: 13
total alignments: 18812558
6000000 reads aligned.
Avg alignment size: 13
total alignments: 20461447
Avg alignment size: 13
Avg sparse alignment size: 4
21155208 alignments calculated.
Round 1 takes 6022 secs.
Calculating reads overlaps, round 2
1000000 reads aligned.
Avg alignment size: 13
total alignments: 730047
2000000 reads aligned.
Avg alignment size: 14
total alignments: 1574683
3000000 reads aligned.
Avg alignment size: 14
total alignments: 2453497
4000000 reads aligned.
Avg alignment size: 14
total alignments: 3703999
5000000 reads aligned.
Avg alignment size: 15
total alignments: 4870288
6000000 reads aligned.
Avg alignment size: 15
total alignments: 6172716
Avg alignment size: 15
Avg sparse alignment size: 4
6825258 alignments calculated.
Round 2 takes 246 secs.
5698522 contained out of 6444911
37006 tips in the graph.
Graph simplification.
Iteration: 0
149180 branching positions.
242683 linear nodes.
Iteration: 1
72771 branching positions.
285918 linear nodes.
Iteration: 2
17663 branching positions.
326663 linear nodes.
Iteration: 3
17055 branching positions.
326798 linear nodes.
118618 edges deleted.
782865 chimeric reads deleted.
4522 bad nodes removed in aggrassive cleaning.
17931 tips in the graph.
Loading contigs.
Collecting information for consensus.
6444911 reads.
Calculating reads overlaps.
1000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 10332925
2000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 24091984
3000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 38803830
4000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 62439606
5000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 81550159
6000000 reads aligned.
Avg alignment size: 15
Avg sparse alignment size: 2
total alignments: 106241553
Avg alignment size: 15
Avg sparse alignment size: 2
119073335 alignments calculated.
2040 secs.
Loading non-contained sequences.
1131563 loaded.
frag sum: -32138330
offset sum: 1148349553
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