Dear All,
i'm using pbjelly to gapclose an assembly. however, when i run the assemlby stage, the mapping is running but only the mapping because the assembly stage is not closing gaps but only replacing Ns with more accurate numbers of Ns. if i type
Jelly.py assembly --help
i get
1: WrapAssembly.py: not found
i checked in the bin folder and the WrapAssembly.py is not there for the 13.10.22 version while it is there for the 12.9.4.
However, if i run the OLCAssembler in each folder after the extraction stage i get an output for the version 13.10.22.
i'm using wgs-8 and smrtanalysis 2.1 which are both the latest versions.
any idea what is wrong?
thanks
luigi
Luigi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The first behavior you're describing is a bug. I'll put in a ticket to get it fixed. If you want to see the assembly step's help, try
Assembly.py --help
Also, OLCAssembly doesn't work with SMRTAnalysis 2.1. PacBio Deprecated the Allora assembly engine, which previously was used by PBJelly.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
But then my point is: it is OLCAssembly required in the new version of pbjelly? Actually the problem is that software version 13.10.22 works fine on the test set but it is not able to close gaps on my data set. It only places the right amount of Ns at the gap place. Does the latest version uses Amos software like make-consensus? I really do not know why is not working.
Luigi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear All,
i'm using pbjelly to gapclose an assembly. however, when i run the assemlby stage, the mapping is running but only the mapping because the assembly stage is not closing gaps but only replacing Ns with more accurate numbers of Ns. if i type
Jelly.py assembly --help
i get
1: WrapAssembly.py: not found
i checked in the bin folder and the WrapAssembly.py is not there for the 13.10.22 version while it is there for the 12.9.4.
However, if i run the OLCAssembler in each folder after the extraction stage i get an output for the version 13.10.22.
i'm using wgs-8 and smrtanalysis 2.1 which are both the latest versions.
any idea what is wrong?
thanks
luigi
Luigi
The first behavior you're describing is a bug. I'll put in a ticket to get it fixed. If you want to see the assembly step's help, try
Assembly.py --help
Also, OLCAssembly doesn't work with SMRTAnalysis 2.1. PacBio Deprecated the Allora assembly engine, which previously was used by PBJelly.
But then my point is: it is OLCAssembly required in the new version of pbjelly? Actually the problem is that software version 13.10.22 works fine on the test set but it is not able to close gaps on my data set. It only places the right amount of Ns at the gap place. Does the latest version uses Amos software like make-consensus? I really do not know why is not working.
Luigi