Question: Tophat Error: segment-based junction search failed with err =1
0
gravatar for a.turtoi
15 months ago by
a.turtoi50
a.turtoi50 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 • 526 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by a.turtoi50
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 15 months ago by Jennifer Hillman Jackson23k
0
gravatar for a.turtoi
15 months ago by
a.turtoi50
a.turtoi50 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 COMMENTlink written 15 months ago by a.turtoi50

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 REPLYlink written 15 months ago by Jennifer Hillman Jackson23k
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