Hi,
I am doing do novo assembly of a bacterial genome ~4Mb. I used Abyss and it took around 8 hours to produce ~1000 scaffolds (N50 80kb).
I used paired-end reads 100bp (total ~300,000,000 reads), mate-paired reads 100 bp (~60,000,000 reads total) and long single end reads ~3kb with 50x coverage. SOAPdenovo has been running for 48 hours now on Linux 64-bit with 8 cpus and 33GB RAM.
Is this running time normal? The log by now says: 32400000000th reads. I don't know long the program will take to finish the analysis, is there any way of seeing this?
Thanks
I am doing do novo assembly of a bacterial genome ~4Mb. I used Abyss and it took around 8 hours to produce ~1000 scaffolds (N50 80kb).
I used paired-end reads 100bp (total ~300,000,000 reads), mate-paired reads 100 bp (~60,000,000 reads total) and long single end reads ~3kb with 50x coverage. SOAPdenovo has been running for 48 hours now on Linux 64-bit with 8 cpus and 33GB RAM.
Is this running time normal? The log by now says: 32400000000th reads. I don't know long the program will take to finish the analysis, is there any way of seeing this?
Thanks
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