PreAssembler module no corrected.fasta output

[zhoufan]

Hi,
I am using smrtpipe 2.0 for de novo assembly.when using preAssembler moudule to error correct the long reads with illumina short reads,there is no corrected.fasta output. I've searched into the log file,there is no error and just one Warning saying" could not load /smrtanalysis/analysis/lib/graphviz/libgvplugin_pango.so.6-file not found".
I went to the /smrtanalysis/analysis/lib/graphviz dir found that the "libgvplugin_pango.so.6" is linked to 'libgvplugin_xlib.so.6.0.0'.
The parameters used in this module is attched.

help is greatly appreciated!

[rhall]

Can you post your input.xml, and log files, master.log, smrtpipe.log.
Thanks.

[zhoufan]

Hi rhall,
Thank you for your reply.I attached the input.xml,param.xml,master.log and smrtpipe.log. The master.log is a little huge for this website,so i tailed it ,hope it includes all the useful information.

[rhall]

The smrtpipe.log and the master.log do not show SMRT pipe exiting, either failing or completing. The last task to execute is layout, you can try executing it manually using the ./workflow/P_PreAssembler/layout.sh script. Also I would suggest pointing a browser at ./workflow/Workflow.summary.html it will display the execution graph. It is possible to see the order of executed tasks, you can then run the tasks manually to see which one stalls.

[zhoufan]

Thanks! I started a new run and seccussed. It may because wrong operation to the computer.