Too few PE links

[Ferdi]

Hi - 

I'm assembling an invertebrate genome of ~500Mb using SOAPdenovo2. For the scaffolding, I have 3 mate-pair libraries (~3kb, ~5kb and ~6kb). The scaffolding stage goes though but the logfile shows worrying error messages which seems to indicate that 2 of the mate-pair libraries are rejected because of 'Too few PE links' (see attach extract). The third one seems ok and gives a decent scaffolding. However I'm puzzled why these 2 libraries didn't pass the filter. 

 I independently mapped the mate-pair to contigs and compute the size distribution to check how look these libraries  (see graph below). From my understanding of how SOAP works, it starts to gather all connections on contigs larger that the library average size indicated and used them for redefine library average size. From the distribution, there should be enough of such connections, at least for the library of 3kb to satisfy this criterion. I'd like to better understand which filters the PE link have to pass!  I tried to play with the indicated average size in the config file to see if it was changing something but it didn't. 

I appreciate your help and feedback on that issue. Maybe my libraries are not indeed bad but I'd then like to understand what is the exact problem. 

Ferdi

For insert size: 3250
 Total PE links                      23061301
 Normal PE links on same contig      96
 Incorrect oriented PE links         19
 PE links of too small insert size   1371194
 PE links of too large insert size   0
 Correct PE links                    21689741
 Accumulated connections             43379084
Use contigs longer than 3250 to estimate insert size:
 PE links               77
Too few PE links.
21689542 new connections.
For insert size: 5000
 Total PE links                      24097524
 Normal PE links on same contig      152439
 Incorrect oriented PE links         1085
 PE links of too small insert size   115289
 PE links of too large insert size   0
 Correct PE links                    22131611
 Accumulated connections             13431114
Use contigs longer than 5000 to estimate insert size:
 PE links               97055
 Average insert size    5322
 SD                     834
6715557 new connections.
For insert size: 5700
 Total PE links                      21348956
 Normal PE links on same contig      20
 Incorrect oriented PE links         22
 PE links of too small insert size   181047
 PE links of too large insert size   0
 Correct PE links                    21167615
 Accumulated connections             42334634
Use contigs longer than 5700 to estimate insert size:
 PE links               7
Too few PE links.
21167317 new connections.