I'm running Newbler 2.3 on an Ubuntu box (MacPro, dual quad core, 32 Gb RAM) and having some issues. Wondering if anyone out there is using Ubuntu and experiencing similar problems?
Everything appears to be working w.r.t. the GUI and the app., especially if I run in genome assembly mode as a complex genome, which seems to work fine. However, when I try to run in cDNA mode (I'm doing de novo transcriptome assembly) it takes forever on even relatively small jobs (2-3 gig 454 data). The exact same data run on a RedHat install takes ~30 min.
If I try to do a hybrid assembly with ca. 5xe6 seqs (12 gB data), it always stalls during detangling, ~ 55% complete), loses contact with the GUI, and locks one of my cores @ 100% and my RAM @ ~ 14 Gb. I can exit the app., but I have to reboot to free up the core and the RAM.
Any thoughts/suggestions as to why the cDNA algorithm won't run properly on an Ubuntu install? Roche tech support is working with me, but so far no fixes.
Everything appears to be working w.r.t. the GUI and the app., especially if I run in genome assembly mode as a complex genome, which seems to work fine. However, when I try to run in cDNA mode (I'm doing de novo transcriptome assembly) it takes forever on even relatively small jobs (2-3 gig 454 data). The exact same data run on a RedHat install takes ~30 min.
If I try to do a hybrid assembly with ca. 5xe6 seqs (12 gB data), it always stalls during detangling, ~ 55% complete), loses contact with the GUI, and locks one of my cores @ 100% and my RAM @ ~ 14 Gb. I can exit the app., but I have to reboot to free up the core and the RAM.
Any thoughts/suggestions as to why the cDNA algorithm won't run properly on an Ubuntu install? Roche tech support is working with me, but so far no fixes.
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