Question: Failed job "Tophat"
gravatar for tran_tim
2.2 years ago by
tran_tim10 wrote:

Fatal error: Tool execution failed

[2016-09-27 02:31:32] Beginning TopHat run (v2.1.0)

[2016-09-27 02:31:32] Checking for Bowtie Bowtie version: [2016-09-27 02:31:32] Checking for Bowtie index files (genome).. [2016-09-27 02:31:32] Checking for reference FASTA file [2016-09-27 02:31:32] Generating SAM header for /galaxy/data/hg19/hg19full/bowtie2_index/hg19full [2016-09-27 02:31:48] Preparing reads left reads: min. length=100, max. length=100, 38063721 kept reads (0 discarded) [2016-09-27 02:45:47] Mapping left_kept_reads to genome hg19full with Bowtie2 [main_samview] truncated file. [2016-09-27 02:58:51] Mapping left_kept_reads_seg1 to genome hg19full with Bowtie2 (1/4) [2016-09-27 02:59:58] Mapping left_kept_reads_seg2 to genome hg19full with Bowtie2 (2/4) [2016-09-27 03:01:02] Mapping left_kept_reads_seg3 to genome hg19full with Bowtie2 (3/4) [2016-09-27 03:02:05] Mapping left_kept_reads_seg4 to genome hg19full with Bowtie2 (4/4) [2016-09-27 03:03:07] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err =1 Error: could not get read# 8793971 from stream!

ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.2 years ago by tran_tim10

I got the following error above after running Tophat on a Fastq files.What is wrong?

ADD REPLYlink written 2.2 years ago by tran_tim10
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This was probably related to the same cluster issue that caused this problem and this one over the last day or so.

The first-pass solution for all is the same: rerun the failed jobs now

Others that encountered odd tool failures in the last 24hrs at should also try a re-run now.

If problems persist with this same error, please check other recent posts first for feedback from our team.

If your issue/error is different and not resolved by confirming inputs, examining prior Galaxy Biostars Q&A, or by reviewing Support topics here:

  • Post a new question here with the complete error message. Note where you are using Galaxy by URL or the Galaxy version if using a local or cloud Galaxy. The more details included, the easier it is for the community to help troubleshoot.
  • Send in a bug report for 1-1 feedback/help. Bug reports are an alternate help option for novel tool errors requiring history access when using How-to:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson25k
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