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  • sparse_pregraph in SOAPdenovo2

    Hi!

    I'm new to the seqanswers and a novice at genome assembly. I am trying to use SOAPdenovo2, but I am stuck on sparse_pregraph.

    I use this syntax:

    nohup SOAPdenovo-63mer sparse_pregraph -s eurostag2.config -K 35 -z 600000000 -d 1 -e 1 -g 15 -r 0 -p 10 -o eurowolb > pregraph.err 2> pregraph.log &

    I have what appears to me to be a valid config file in the appropriate folder, but I keep getting Exit 255.

    My data are Illumina paired end reads (4 pairs of files), and 4 single end file that were are orphaned reads generated by Corrector_HA in the SOAPdenovo2 pipeline.

    Any suggestions on getting unstuck would be appreciated.

    Ed

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