Hi Vipin, It appears that the index file for your input bam file does not exist. Could you tell me what the process you used to create that bam file was? The index file is supposed to be created behind the scenes when SAM-to-BAM is run--did you encounter any problem at that point? Regards, Kelly On Nov 10, 2009, at 8:46 AM, Vipin TS wrote:

Hi all,

I am trying to run 'Generate pileup' tool from NGS: SAM Tool tracks in local galaxy instance. I am getting the desired output and the job status ends with and error message.

Here is the error message:

An error occurred running this job: cp: cannot stat `/home/galaxy/ galaxy-2.1.2009/database/files/_metadata_files/000/metadata_4.dat': No such file or directory

I compared the result from my local instance with main galaxy server and there is no difference at all. Please let me know anything wrong in my side.

Many thanks in advance, Vipin T S

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