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Troubleshooting Batch Problems

License problems

If you get a license error when you try to run a third-party software application, it means either the licenses are all in use or you’re not on the access list for the license. Very rarely there could be a problem with the license server. You should read the software page for the application you’re trying to use and make sure you’ve complied with all the procedures and are correctly requesting the license. Contact OSC Help with any questions.

My job is running slower than it should

Here are a few of the reasons your job may be running slowly:

Batch-Related Command Summary

This section summarizes two groups of batch-related commands: commands that are run on the login nodes to manage your jobs and commands that are run only inside a batch script. Only the most common options are described here.

Many of these commands are discussed in more detail elsewhere in this document. All have online manual pages (example: man qsub) unless otherwise noted.

In describing the usage of the commands we use square brackets [like this] to indicate optional arguments. The brackets are not part of the command.

Batch Environment Variable Summary

The batch system provides several environment variables that you may want to use in your job script. This section is a summary of the most useful of these variables. Many of them are discussed in more detail elsewhere in this document. The ones beginning with PBS_ are described in the online manual page for qsub (“man qsub”).

PBS Directives Summary

PBS directives may appear as header lines in a batch script or as options on the qsub command line. They specify the resource requirements of your job and various other attributes. Many of the directives are discussed in more detail elsewhere in this document. The online manual page for qsub (man qsub) describes many of them.

PBS header lines must come before any executable lines in your script. Their syntax is:

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.

EMBOSS

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:

  • Sequence alignment,
  • Rapid database searching with sequence patterns,
  • Protein motif identification, including domain analysis,
  • Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
  • Codon usage analysis for small genomes,
  • Rapid identification of sequence patterns in large scale sequence sets,
  • Presentation tools for publication

Clustal W

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.

BLAT

BLAT is a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes.

BLAST

The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.

Bioperl

Bioperl offers a set of perl modules which can be used for sequence manipulation. Knowledge of PERL programming is required.

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