HGAP issue in smrtanalysis 2.0.1

[schroedj]

I'm trying to assemble a bacterial genome (about 4.1Mbases in length) using HGAP in smrtanalysis 2.0.1. The job runs until the draft assembly is finished and then fails after that point. I am at a loss as to how to fix this problem. I am running this on a single node machine. I have attached the master.log and smrtpipe.log files. I would really appreciate any help I can get with this matter.

I should mention that I've run HGAP on the included lambda SMRT cell and it does get all the way to a polished genome, so it seems to me that I have smrtanalysis set up correctly on my system.

[schroedj]

Sorry for the noise, but I just found the issue.... In the log/P_Mapping/align.log file, it says "/tmp/sortg5zIfL: No space left on device". Clearly, my /tmp directory is full. Can I change the location to which Smrtanalysis saves temporary files at this point, or do I have to reconfigure the installation and set the new location during the initial configuration?

Thanks.

[mjhsieh]

Sorry for the noise, but I just found the issue.... In the log/P_Mapping/align.log file, it says "/tmp/sortg5zIfL: No space left on device". Clearly, my /tmp directory is full. Can I change the location to which Smrtanalysis saves temporary files at this point, or do I have to reconfigure the installation and set the new location during the initial configuration?

Thanks.

I think you can edit the file in analysis/etc/smrtpipe.rc and find "TMP = " entry and set it to a directory according to number four of this section:

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation-v2.0.1#network-file-system-requirement

[GenoMax]

I think you can edit the file in analysis/etc/smrtpipe.rc and find "TMP = " entry and set it to a directory according to number four of this section:
https://github.com/PacificBioscience...em-requirement

Remember to bounce the application after making the change noted above.

[schroedj]

I have to say, I'm a little embarassed to have missed what was so clearly written in the documentation. After changing the TMP variable, HGAP ran to completion with one 4Mbase contig.

Thanks for the help.