I'm trying to map a data set containing 454 reads to a reference genome
using LASTZ alignment package in Galaxy. I'm following a workflow used for
Illumina reads with the only change in the alignment package, i'm using
LASTZ instead of bowtie/bwa. The following is the procedure please correct
me if it's wrong and do suggest any additional procedure to make the
workflow better.

In addition to this i'm, trying to do metagenomics analysis as well
by following the procedure given in one of the video tutorials. I've
submitted the files for alignment and its been a day since the submission
and the process has not yet started, could you tell me what could be the
reason. The file size is 110Mb, under history the package indicate  "Job is
waiting run"  how long does it usually take to initiate the process in the
queue. Your suggestion's are valuable, thanks for developing Galaxy.

Kindly help, thank you.

1.Uploaded a FASTA file as input
2.Align using LASTZ
3.Filtering SAM files on bit-wise flag values
4.Finding how many reads are mapped to each chromosome
5.Sort the read counts
6.convert sam to bam
7.perform flagstat operation

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