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  • HGAP issue in smrtanalysis 2.0.1

    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.

  • #2
    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.

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    • #3
      Originally posted by schroedj View Post
      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:
      GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.

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      • #4
        Originally posted by mjhsieh View Post
        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.

        Comment


        • #5
          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.

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