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Question: Error: Remote job server indicated a problem running or monitoring this job
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gravatar for kelly.hudspeth
10 months ago by
kelly.hudspeth • 0
kelly.hudspeth • 0 wrote:

Hi I keep running into this error: Remote job server indicated a problem running or monitoring this job when running tophat for RNASeq data. It says it is a tool error. What does this mean?

Thanks Kelly
rna-seq tophat2 software error tophat hisat2 • 306 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by kelly.hudspeth • 0

The problem is probably due to one of these common input issues (not all clusters report the more specific error messages). Please double check your data inputs against the list to start troubleshooting: https://galaxyproject.org/support/tool-error/

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I double checked your job. The same dataset (number 24) was input for both the forward and reverse reads of the pair.

In this tutorial, the reads with a _1 are forward and with a _2 are reverse. There are four fastq datasets that combine to make two pairs. Run the QA/trimming steps on all four, then run Tophat in paired-end mode using one of the pairs (two fastq inputs). Then run Tophat on the other pair (the remaining two fastq inputs). Later on, you can learn how to do batch job submission in the tutorials linked below.

The tutorial you are using is older and still functions correctly as far as I know. Just be aware that Tophat/Tophat2 is considered deprecated now and replaced by HISAT2, so after learning and ready to do your own analysis, you'll want to use the latest tools and workflows.

Galaxy tutorials (the most current): https://galaxyproject.org/learn/

Support FAQs: https://galaxyproject.org/support/#troubleshooting. Start here next time you have a job fail: My job ended with an error. What can I do?

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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