Version 2.04: released on July 13th, 2012
Compile Jul 31 2013	00:50:50

********************
Map
********************

Parameters: map -k 61 -g ./ -s soapdenovo2.config -p 32

Kmer size: 61.
Contig length cutoff: 63.

23786991 contig(s), maximum sequence length 32494, minimum sequence length 62, maximum name length 10.
Time spent on parsing contigs file: 20s.
32 thread(s) initialized.
--- 10000000th contig(s).
--- 20000000th contig(s).
Time spent on hashing contigs: 818s.
2750818010 node(s) allocated, 2792495157 kmer(s) in contigs, 2792495157 kmer(s) processed.
Time spent on graph construction: 838s.

Time spent on aligning long reads: 0s.

In file: soapdenovo2.config, max seq len 200, max name len 256
32 thread(s) initialized.
47570951 edge(s) in the graph.
Import reads from file:
 ../MD_NoIndex_R1.clipped.fastq
Import reads from file:
 ../MD_NoIndex_R2.clipped.fastq
Current insert size is 200, map_len is 32.
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.
--- 400000000th reads.
--- 500000000th reads.
--- 600000000th reads.
--- 700000000th reads.
Import reads from file:
 ../M273_R1.clipped.fastq
Import reads from file:
 ../M273_R2.clipped.fastq
Current insert size is 2859, map_len is 35.
--- 800000000th reads.
--- 900000000th reads.
Import reads from file:
 ../8kbp/nextclip/nextclipped_ABC_R1.fastq
Import reads from file:
 ../8kbp/nextclip/nextclipped_ABC_R2.fastq
Current insert size is 6455, map_len is 35.
--- 1000000000th reads.
--- 1100000000th reads.

Total reads         1158827266
Reads in gaps       294860842
Ratio               25.4%
Reads on contigs    889879899
Ratio               76.8%
3 pe insert size, the largest boundary is 1158827266.

LIB(s) information:
 [LIB] 0, avg_ins 200, reverse 0.
 [LIB] 1, avg_ins 2859, reverse 1.
 [LIB] 2, avg_ins 6455, reverse 1.
Time spent on aligning reads: 14598s.

Overall time spent on alignment: 257m.




Version 2.04: released on July 13th, 2012
Compile Jul 31 2013	00:50:50

********************
Scaff
********************

Parameters: scaff -g ./ -p 32

Files for scaffold construction are OK.

There are 3 grad(s), 1158827266 read(s), max read len 200.
Kmer size: 61
There are 47570951 edge(s) in edge file.
Mask contigs with coverage lower than 1.3 or higher than 26.0, and strict length 0.
Average contig coverage is 13, 8470696 contig(s) masked.
Mask contigs shorter than 63, 28685846 contig(s) masked.
66682006 arc(s) loaded, average weight is 8.
23786991 contig(s) loaded.
Done loading updated edges.
Time spent on loading updated edges: 594s.

File ./.links exists, skip creating the links...
Time spent on loading paired-end reads information: 0s.

*****************************************************
Start to construct scaffolds.

***************************
For insert size: 200
 Total PE links                28499852
 PE links to masked contigs    22395026
 On same scaffold PE links     0
Cutoff of PE links to make a reliable connection: 3
 Active connections    12209652
 Weak connections      6963500
 Weak ratio            57.0%
21 circles removed.
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37156626
Remained contigs                      10414325
None-outgoing-connection contigs      5737303 (55.090492%)
Single-outgoing-connection contigs    4148410
Multi-outgoing-connection contigs     39334
Cycle 1
 Two-outgoing-connection contigs     489278
 Potential transitive connections    2199
 Transitive connections              1804
 Transitive ratio                    0.4%
Cycle 2
 Two-outgoing-connection contigs     487045
 Potential transitive connections    395
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          411988
 Connection-conflict        29
 Significant overlapping    158114
 Eligible                   41
 Bubble structures          16881
Mask repeats:
 Puzzles           127843
 Masked contigs    117381
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37425150
Remained contigs                      10145801
None-outgoing-connection contigs      5759897 (56.771244%)
Single-outgoing-connection contigs    4376155
Multi-outgoing-connection contigs     654
Cycle 1
 Two-outgoing-connection contigs     9095
 Potential transitive connections    71
 Transitive connections              57
 Transitive ratio                    0.6%
Cycle 2
 Two-outgoing-connection contigs     9030
 Potential transitive connections    14
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          9659
 Connection-conflict        0
 Significant overlapping    9226
 Eligible                   0
 Bubble structures          3
Start to mask puzzles.
 Masked contigs      8998
 Remained puzzles    12
Freezing done.

Rank 1
 Scaffold number                  867461
 In-scaffold contig number        7796298
 Total scaffold length            2016384286
 Average scaffold length          2324
 Filled gap number                873088
 Longest scaffold                 107445
 Scaffold and singleton number    5615107
 Scaffold and singleton length    2737707245
 Average length                   487
 N50                              3071
 N90                              150

Report from smallScaf: 867414 scaffolds by smallPE.
***************************
For insert size: 2859
 Total PE links                21681942
 PE links to masked contigs    7708118
 On same scaffold PE links     1455764
Cutoff of PE links to make a reliable connection: 5
Report from checkScaf: 8 scaffold segments broken.
Add large insert size PE links: 854398 orientation-conflict links, 905565 contigs acrossed by normal links.
 Active connections    17038298
 Weak connections      15969396
 Weak ratio            93.7%
13804 circles removed.
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37494280
Remained contigs                      10076671
None-outgoing-connection contigs      5160234 (51.209713%)
Single-outgoing-connection contigs    4255688
Multi-outgoing-connection contigs     113712
Cycle 1
 Two-outgoing-connection contigs     547037
 Potential transitive connections    186329
 Transitive connections              35895
 Transitive ratio                    6.6%
Cycle 2
 Two-outgoing-connection contigs     509353
 Potential transitive connections    149703
 Transitive connections              143
 Transitive ratio                    0.0%
Cycle 3
 Two-outgoing-connection contigs     509211
 Potential transitive connections    149560
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          309742
 Connection-conflict        13641
 Significant overlapping    109115
 Eligible                   319
 Bubble structures          0
Mask repeats:
 Puzzles           61845
 Masked contigs    40279
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37574838
Remained contigs                      9996113
None-outgoing-connection contigs      5040844 (50.428040%)
Single-outgoing-connection contigs    4939912
Multi-outgoing-connection contigs     1121
Cycle 1
 Two-outgoing-connection contigs     14236
 Potential transitive connections    8742
 Transitive connections              2592
 Transitive ratio                    18.2%
Cycle 2
 Two-outgoing-connection contigs     11639
 Potential transitive connections    6158
 Transitive connections              20
 Transitive ratio                    0.2%
Cycle 3
 Two-outgoing-connection contigs     11618
 Potential transitive connections    6137
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          11753
 Connection-conflict        548
 Significant overlapping    8863
 Eligible                   13
 Bubble structures          0
Start to mask puzzles.
 Masked contigs      6794
 Remained puzzles    18
Freezing done.

Rank 2
 Scaffold number                  302725
 In-scaffold contig number        7796298
 Total scaffold length            2773787603
 Average scaffold length          9162
 Filled gap number                799110
 Longest scaffold                 569417
 Scaffold and singleton number    5280753
 Scaffold and singleton length    3364161779
 Average length                   637
 N50                              32506
 N90                              181

***************************
For insert size: 6455
 Total PE links                9406544
 PE links to masked contigs    3133960
 On same scaffold PE links     2546886
Cutoff of PE links to make a reliable connection: 5
Report from checkScaf: 82 scaffold segments broken.
Add large insert size PE links: 3833 orientation-conflict links, 1206400 contigs acrossed by normal links.
 Active connections    3459424
 Weak connections      3162810
 Weak ratio            91.4%
3591 circles removed.
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37592094
Remained contigs                      9978857
None-outgoing-connection contigs      4736266 (47.463013%)
Single-outgoing-connection contigs    4639735
Multi-outgoing-connection contigs     109096
Cycle 1
 Two-outgoing-connection contigs     493760
 Potential transitive connections    275175
 Transitive connections              36141
 Transitive ratio                    7.3%
Cycle 2
 Two-outgoing-connection contigs     451582
 Potential transitive connections    236758
 Transitive connections              217
 Transitive ratio                    0.0%
Cycle 3
 Two-outgoing-connection contigs     451331
 Potential transitive connections    236537
 Transitive connections              1
 Transitive ratio                    0.0%
Cycle 4
 Two-outgoing-connection contigs     451329
 Potential transitive connections    236536
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          212131
 Connection-conflict        11498
 Significant overlapping    70429
 Eligible                   87
 Bubble structures          0
Mask repeats:
 Puzzles           35773
 Masked contigs    15434
Start to remove transitive connection.
Total contigs                         47570951
Masked contigs                        37622962
Remained contigs                      9947989
None-outgoing-connection contigs      4629076 (46.532784%)
Single-outgoing-connection contigs    5302339
Multi-outgoing-connection contigs     2458
Cycle 1
 Two-outgoing-connection contigs     14116
 Potential transitive connections    10641
 Transitive connections              981
 Transitive ratio                    6.9%
Cycle 2
 Two-outgoing-connection contigs     13084
 Potential transitive connections    9643
 Transitive connections              6
 Transitive ratio                    0.0%
Cycle 3
 Two-outgoing-connection contigs     13078
 Potential transitive connections    9637
 Transitive connections              0
 Transitive ratio                    0.0%
Start to linearize sub-graph.
 Picked sub-graphs          14047
 Connection-conflict        1178
 Significant overlapping    10798
 Eligible                   8
 Bubble structures          0
Non-strict linearization.
Start to linearize sub-graph.
 Picked sub-graphs          8464
 Connection-conflict        476
 Significant overlapping    4680
 Eligible                   5
 Bubble structures          0
Start to mask puzzles.
 Masked contigs      2910
 Remained puzzles    6
Freezing done.

Recover contigs.
 Total recovered contigs    3941
 Single-route cases         3862
 Multi-route cases          25

All links loaded.
Time spent on constructing scaffolds: 1490s.

The final rank

*******************************
 Scaffold number                  173731
 In-scaffold contig number        7796298
 Total scaffold length            3149534025
 Average scaffold length          18128
 Filled gap number                765713
 Longest scaffold                 1740577
 Scaffold and singleton number    5085141
 Scaffold and singleton length    3701554035
 Average length                   727
 N50                              155749
 N90                              214
 Weak points                      37

*******************************
1000 scaffolds processed.
[...]