Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using Galaxy through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19. Here's the error: An error occurred running this job: *cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.050000 -b /galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g* Thanks for the help. -- Erin Shanle Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 shanle@wisc.edu
Hello Erin, This was a temporary problem due to a new filesystem we installed during this time frame, that has since been resolved. Please try again and if the problem persists, please send a bug report from the error dataset using the green bug icon. This allows us to gain access to the inputs and job parameters to diagnose the root cause of the problem. http://wiki.g2.bx.psu.edu/Support#Error_from_tools http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Thank you! Jen Galaxy team On 1/20/12 6:51 AM, Erin Shanle wrote:
Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using Galaxy through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19. Here's the error:
An error occurred running this job: /cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.050000 -b /galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g/
Thanks for the help. -- Erin Shanle
Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 shanle@wisc.edu <mailto:shanle@wisc.edu>
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participants (2)
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Erin Shanle -
Jennifer Jackson