Failed job "Tophat"

Question: Failed job "Tophat"

2.2 years ago by

tran_tim • 10 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: 2.2.5.0 [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!

error tool tophat cluster usegalaxy.org • 684 views

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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by tran_tim • 10

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

ADD REPLY • link written 2.2 years ago by tran_tim • 10

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This was probably related to the same cluster issue that caused this problem https://biostar.usegalaxy.org/p/19754/ and this one https://biostar.usegalaxy.org/p/19740/ 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 http://usegalaxy.org 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 http://usegalaxy.org. How-to: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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

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