Question: Problem with running TopHat and MARKDuplicates on Galaxy
2
gravatar for Genosis
19 months ago by
Genosis20
Genosis20 wrote:

To galaxy experts, I would like to ask your advice on some problems I've been encountering with running my dataset on Galaxy. I have a set of paired end reads from Illumina HisEq which I have uploaded and attempt to run a workflow by TRAPLINE and is currently stuck with a few error messages:

  1. MarkDuplicates on data no. X -Mark duplicate metrics X (this happens to all my output sample files) Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 10: null:HWI-ST513:514:C98LLACXX:7:1315:16207:46727

  2. MarkDuplicates on data No.X - Mark duplicates BAM output (This happens to all my updated sample files) Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 10: null:HWI-ST513:514:C98LLACXX:7:1315:16207:46727

  3. TOPHAT : accepted hits. - Happens only to 1 of my data files. This function generated an error message. I am not sure why but when I checked, it attempts to use a mouse database. Despite trying multiple times changing back to human, mouse is still being selected by the program. Whenever I try to change the species, the following message pops up on top "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." I checked and ensure the dataset is not currently 'running' and 'being used', but the same error message persists.

I would appreciate any advice you may have Thank you

ADD COMMENTlink written 19 months ago by Genosis20

Hello, The problem is likely with the inputs, but I'll run a test with the workflow as it exists at http://usegalaxy.org. More feedback once that is completed (may take a day to process all steps). Jen, Galaxy team

ADD REPLYlink written 19 months ago by Jennifer Hillman Jackson23k

I have the same problem, at this time with point number 3... Any possible solutions? Thanks in advance.

ADD REPLYlink written 8 months ago by obbedio0
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