search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
752 stars 136 forks source link

Yet another: finished abnormally, err code: -6 #217

Closed lavik17 closed 5 years ago

lavik17 commented 5 years ago

I've collected paired and single reads that were mapped to a metagenome-resolved bin, and I am now trying to reassemble the bin using either spades or metaspades.

I am running it on a machine with 250Gb of RAM available and 48 threads. spades.log and params.txt are attached.

Thank you for your help!

Adi params.txt [Uploading spades.log…]()

asl commented 5 years ago

Please upload your spades.log file

lavik17 commented 5 years ago

wops, it didn't go through. Here it is spades.log

Thanks Anton!

lavik17 commented 5 years ago

I had some progress. The error did not repeat itself when I used a larger kmer as a starting point ( -k 41,61,81,101,121) with only the paired reads. However, I did get a similar error code when running with paired as well as unpaired reads.

asl commented 5 years ago

So, here what happened: you feed to SPAdes some arbitrary set of reads (likely corresponding to some bin of poor quality of something like this). The set consisted of ~30k paired-end reads (so unlikely to be any metagenome or even non-trivial part of it). The final assembly graphs consists of 16639 edges and almost no paired-end reads aligned to the long edges of the graph as a whole:

  0:01:14.069     1G / 30G   INFO    General                 (pair_info_count.cpp       : 213)   15 paired reads (0.0494641% of all) aligned to long edges
  0:01:14.114   256M / 30G   INFO    General                 (pair_info_count.cpp       : 354)     Insert size = 283.4, deviation = 170.967, left quantile = 74, right quantile = 562, read length = 151

This might be due to two reasons:

  1. You left reads do not correspond to the right ones
  2. The graph consists of just huge pile of short isolated edges