can't find GenomePath

[ghost]

I'm trying to run Pisces on centOS.

I run the command:

mono /opt/Pisces_5.1.6.54/Pisces.exe -G /data/atimms/references/human_g1k_v37.fasta -Bam LR04-350.bwa_gatk.bam -GenomePaths /data/atimms/references/human_g1k_v37.fasta

but get the error message:

Unhandled Exception: System.Exception: Unable to process: GenomePath '/data/atimms/references/human_g1k_v37.fasta' does not exist. ---> System.ArgumentException: GenomePath '/data/atimms/references/human_g1k_v37.fasta' does not exist. at Pisces.ApplicationOptions.Validate () [0x001b3] in :0 at Pisces.ApplicationOptions.ParseCommandLine (System.String[] arguments) [0x00011] in :0 at Pisces.Program..ctor (System.String[] args) [0x00006] in :0 at Pisces.Program.Main (System.String[] args) [0x0000b] in :0 --- End of inner exception stack trace --- at Pisces.Program.Main (System.String[] args) [0x00035] in :0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Unable to process: GenomePath '/data/atimms/references/human_g1k_v37.fasta' does not exist. ---> System.ArgumentException: GenomePath '/data/atimms/references/human_g1k_v37.fasta' does not exist. at Pisces.ApplicationOptions.Validate () [0x001b3] in :0 at Pisces.ApplicationOptions.ParseCommandLine (System.String[] arguments) [0x00011] in :0 at Pisces.Program..ctor (System.String[] args) [0x00006] in :0 at Pisces.Program.Main (System.String[] args) [0x0000b] in :0 --- End of inner exception stack trace --- at Pisces.Program.Main (System.String[] args) [0x00035] in :0

Any idea why the genome fasta file can't be found?

Thanks for any help.

Andrew

[tamsen]

Just specify the directory with your .fa file, not the filename. You will also need GenomeSize.xml. http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn

example arg: -g /genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta

[ghost]

thanks for getting back to me, and pisces worked..

Andrew