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i'm merging Illumina paired-end reads with CASPER. For some reason it works for some files and doesn't for others. The terminal print "killed:9". 9 is the return value of os.system (i'm using python). I know CASPER stops merging if :

too many mismatches exist in the overlap (i.e., the mismatch ratio exceeds a user-specified 'give-up' threshold γ), CASPER does not merge the reads.

I've used CASPER with default values options. But i tried to reduce the overlap length in order reduce the possible mismatches but it didn't work. i tried the same with the threshold for mismatch ratio of best overlap region and it also failed.

Andriniaina Andy Nkili Meyong
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  • Is the process running out of memory? You can test this by using top to monitor the process, or use memusg https://gist.github.com/netj/526585. – Vince Mar 31 '15 at 20:08
  • i have figured it out. i had to adjust the size of k-mer and the size of the minimum overlap. My guess is : with default parameters (k-mer and overlap) i had a big overlap and too big k-mers, i think long k-mers allow more possible mismatches when it comes to compare overlap region. that's why CASPER gave the merging up. anyway reducing k-mer size and overlap region did the trick for the rest of my files that didn't work previously – Andriniaina Andy Nkili Meyong Apr 01 '15 at 19:57

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