Question: Tophat Error for SRA accessions
gravatar for chandrugcg_77
4 months ago by
chandrugcg_7710 wrote:

Dear Sir, I have downloaded SRR924323,SRR912644,SRR915924 & SRR915925 from NCBISRA toolhit. All these accessions reads are showing error when analysing through tophat. Kindly clarify this..........

Thanking you,

error tophat mapping rna-seq • 121 views
ADD COMMENTlink written 4 months ago by chandrugcg_7710
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


What is the error? To locate this, click on the green bug icon for one of the red error results from Tophat.

Does it match up with any of the error troubleshooting help here?

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k

If you still need help, please comment back with the error details.

I was able to download all four using the tool Download and Extract Reads in FASTA/Q format from NCBI SRA. That outputs fastqsanger formatted data ready to QA and use with tools.

Galaxy tutorials:

Support FAQs:


ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k

From chandrugcg_77 in a duplicated post:

tool error An error occurred with this dataset: Remote job server indicated a problem running or monitoring this job.

[2018-02-22 05:14:53] Reporting output tracks [FAILED] Error running /cvmfs/ --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 500000.............................................................................

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k


Tophat is a deprecated tool and should now be avoided. HISAT2 is the replacement.

Please be aware that when using HISAT2, setting the strand and the alignment reporting type both need to be specified for the resulting BAM to be used with certain downstream tools (including Stringie/Cufflinks/Cuffdiff).

An example of HISAT2 usage is covered in the Galaxy tutorials:

Should HISAT2 fail with a data/memory/walltime error, then there is either an input problem or the job really is too large to execute at Galaxy Main Check the inputs first, as this is the most common reason for failures. If you cannot determine the reason, please send in a bug report from the HISAT2 job (leaving the error dataset and all inputs undeleted).

How to check for common input problems is in the Galaxy support FAQs:

Thanks, Jen, Galaxy team

ADD REPLYlink written 7 weeks ago by Jennifer Hillman Jackson25k

Update2: The Tophat tool was determined to have a technical issue processing jobs since later last week. This is now corrected.

Should the tool fail with a rerun, it may really be too large to process at, or there may be an input problem. How to check:

Tophat is still considered deprecated with HISAT2 the recommended updated tool.


ADD REPLYlink written 7 weeks ago by Jennifer Hillman Jackson25k
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