Could not parse delta file

[MCH74]

Hi,

I'm getting following output:

args {'mapcontigs': None, 'mummerLink': '/home/h/harrisom/mummer-4.0.0beta2/', 'fast': None, 'folderName': 'FSC_Out/', 'large': None, 'pickup': None, 'parallel': '50'}
Go Bears! ! ! pickupname, mapcontigsname None None removeEmbedded nProc 50 ERROR: Could not parse delta file, FSC_Out/self.delta error no: 402

It has continued to produce output. And even though it appears to be complete from the following output, it is still running:

All done, 1835 seconds elapsed 3 1730575 1836098 7015991 164670 1933670 2618808 All contigs used? True NContig 10704 fillGap >formRelatedReadsFile len(readSet) 10704 nProc 50 50

Any ideas what has gone wrong?

Thanks,
Mark

[kakitone]

Can you try using absolute path for the folder "FSC_Out/" ?

Also, you may want to try FinisherSC on a small dataset to validate installation first before using it on a large dataset. You may find the following link helpful.

#20 (comment)

[MCH74]

Thanks for the tip. The test data set worked. I think my genome might be too big because I'm getting memory issues and producing core... files, even though I'm reserving 180Gb. I'll try it on a more powerful machine.
Thanks,
Mark