Reading input alignment... Found 1 sequences of length 6264404

Reading EMBL file(s)... Reading annotation file...
Guessing file is embl
Trying to open file Pseudomonas_aeruginosa_PAO1_v2.embl as embl
Annotation file successfully read.
Done

Identifying SNPs... Done
Found 0 sites with a SNP
Constant bases:
A: 1056134
C: 2102687
G: 2066633
T: 1038950


Calculating dN/dS values... Done

Writing output file(s).../software/pathogen/external/lib/python2.7/site-packages/biopython-1.59-py2.7-linux-x86_64.egg/Bio/Align/Generic.py:54: BiopythonDeprecationWarning: With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython.
  warnings.warn("With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
 AE004091 excluded from snp alignment as it is < 50% mapped
Done
All finished.


------------------------------------------------------------
Sender: LSF System <lsfadmin@pcs4o>
Subject: Job 652093: </nfs/users/nfs_s/sh16/scripts/summarise_snps.py -i output_PAO1.aln -r AE004091 -o PAO1_output_summary -e Pseudomonas_aeruginosa_PAO1_v2.embl -t -a> Done

Job </nfs/users/nfs_s/sh16/scripts/summarise_snps.py -i output_PAO1.aln -r AE004091 -o PAO1_output_summary -e Pseudomonas_aeruginosa_PAO1_v2.embl -t -a> was submitted from host <pcs4b> by user <ac19> in cluster <pcs4>.
Job was executed on host(s) <pcs4o>, in queue <normal>, as user <ac19> in cluster <pcs4>.
</nfs/users/nfs_a/ac19> was used as the home directory.
</lustre/scratch108/bacteria/ac19/Pseudomonas_fastq_files/PAO1fimL_outputs> was used as the working directory.
Started at Fri Jan 11 16:14:51 2013
Results reported at Fri Jan 11 16:15:31 2013

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
/nfs/users/nfs_s/sh16/scripts/summarise_snps.py -i output_PAO1.aln -r AE004091 -o PAO1_output_summary -e Pseudomonas_aeruginosa_PAO1_v2.embl -t -a
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     37.45 sec.
    Max Memory :      1366 MB
    Max Swap   :      1547 MB

    Max Processes  :         3
    Max Threads    :         4

The output (if any) is above this job summary.