Tophat Error: segment-based junction search failed with err =1

Question: Tophat Error: segment-based junction search failed with err =1

2.1 years ago by

a.turtoi • 50

a.turtoi • 50 wrote:

Hi Everybody,

I have this error message when I try to do Top Hat algorithm on my Groomer FASTQ files....any clue?

Fatal error: Tool execution failed

[2016-10-12 09:52:29] Beginning TopHat run (v2.1.0)

[2016-10-12 09:52:29] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-10-12 09:52:29] Checking for Bowtie index files (genome).. [2016-10-12 09:52:29] Checking for reference FASTA file [2016-10-12 09:52:29] Generating SAM header for /galaxy/data/hg19/hg19full/bowtie2_index/hg19full [2016-10-12 09:52:39] Preparing reads left reads: min. length=35, max. length=76, 57291316 kept reads (7396 discarded) right reads: min. length=35, max. length=76, 57269242 kept reads (29470 discarded) [2016-10-12 10:38:58] Mapping left_kept_reads to genome hg19full with Bowtie2 [2016-10-12 11:54:01] Mapping left_kept_reads_seg1 to genome hg19full with Bowtie2 (1/3) [2016-10-12 12:02:44] Mapping left_kept_reads_seg2 to genome hg19full with Bowtie2 (2/3) [2016-10-12 12:10:46] Mapping left_kept_reads_seg3 to genome hg19full with Bowtie2 (3/3) [2016-10-12 12:20:23] Mapping right_kept_reads to genome hg19full with Bowtie2 [2016-10-12 13:36:01] Mapping right_kept_reads_seg1 to genome hg19full with Bowtie2 (1/3) [2016-10-12 13:47:15] Mapping right_kept_reads_seg2 to genome hg19full with Bowtie2 (2/3) [2016-10-12 13:56:19] Mapping right_kept_reads_seg3 to genome hg19full with Bowtie2 (3/3) [2016-10-12 14:08:22] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err =1 Error: could not get read# 13397441 from stream!

error tophat job rna-seq • 1.1k views

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modified 2.1 years ago • written 2.1 years ago by a.turtoi • 50

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a common place for Tophat to fail when there is a network/filesystem problem (busy, interrupted connection). A re-run will usually correct it.

Similar problems can also occur if the inputs are empty, a genome mismatch is present in the inputs, or the job runs out of memory (although most memory failures are captured with a specific error).

Try the rerun first. Then check your data and if any fixes are made, rerun after. If you cannot find the problem and can reproduce it at http://usegalaxy.org a bug report can be sent in. Leave all data undeleted and include a link to this Biostars post in the comments.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

2.1 years ago by

a.turtoi • 50

a.turtoi • 50 wrote:

Hi Jen,

in fact this failure is the 3rd time on this dataset, so it is not Galaxy. In fact I run all my data with "Mean Inner Distance between Mate Pairs" = 100. This works fine. However, with this data set I had to reduce this to 80 and only then it worked. I find it strange as the sample prep is the same and the sequencing as well. Any idea why this is like this?

Regards Andrei

ADD COMMENT • link written 2.1 years ago by a.turtoi • 50

Interesting, so the problem was that nothing was mapping.

The sample could be problematic. Try running FastQC on it - and the others - and see if anything comes out that points to a content quality issue. It could be that this sample had bad prep, problems in sequencing, or was perhaps over clipped (?) during other QA?

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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[2016-10-12 09:52:29] Beginning TopHat run (v2.1.0)

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