Tophat2 : Error: Segment-Based Junction Search Failed With Err =-11

Question

[Nicolas Rosewick]

Hi,

I tried yesterday tophat 2.0.4 with fusion-search on several on my samples and I have an error in a few of them at the "Searching for junctions via segment mapping" step. My data are paired-end 76bp (illumina). Here's my command. I allowed 10Gb for each tophat job (so maybe the problem is coming from there.. it's not enough).

tophat -r 60 --b2-sensitive --no-convert-bam --splice-mismatches 1 --min-anchor-length 5 --fusion-search --segment-length 20 --bowtie1 --no-coverage-search --fusion-anchor-length 13 --fusion-min-dist 100000 --mate-std-dev 70 --library-type fr-unstranded --output-dir tophat_2_fusion /home/lab/database/bowtie/ref R1.fastq.gz R2.fastq.gz 



[2012-08-29 20:03:33] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-08-29 20:03:33] Checking for Bowtie
          Bowtie version:     0.12.7.0
[2012-08-29 20:03:33] Checking for Samtools
        Samtools version:     0.1.18.0
[2012-08-29 20:03:33] Checking for Bowtie index files
[2012-08-29 20:03:33] Checking for reference FASTA file
    Warning: Could not find FASTA file /home/lab/database/bowtie/ref.fa
[2012-08-29 20:03:33] Reconstituting reference FASTA file from Bowtie index
  Executing: /home/lab/softs/bowtie-0.12.7/bowtie-inspect /home/lab/database/bowtie/ref > tophat_2_fusion/tmp/ref.fa
[2012-08-29 20:42:20] Generating SAM header for /home/lab/database/bowtie/ref
    format:         fastq
    quality scale:     phred33 (default)
[2012-08-29 20:42:22] Preparing reads
     left reads: min. length=76, max. length=76, 14027314 kept reads (37184 discarded)
    right reads: min. length=76, max. length=76, 14048352 kept reads (16146 discarded)
[2012-08-29 21:09:17] Mapping left_kept_reads to genome ref with Bowtie 
[2012-08-29 22:41:09] Mapping left_kept_reads_seg1 to genome ref with Bowtie (1/3)
[2012-08-29 23:47:18] Mapping left_kept_reads_seg2 to genome ref with Bowtie (2/3)
[2012-08-30 00:54:31] Mapping left_kept_reads_seg3 to genome ref with Bowtie (3/3)
[2012-08-30 01:09:06] Mapping right_kept_reads to genome ref with Bowtie 
[2012-08-30 02:29:13] Mapping right_kept_reads_seg1 to genome ref with Bowtie (1/3)
[2012-08-30 03:38:27] Mapping right_kept_reads_seg2 to genome ref with Bowtie (2/3)
[2012-08-30 04:49:32] Mapping right_kept_reads_seg3 to genome ref with Bowtie (3/3)
[2012-08-30 05:05:35] Searching for junctions via segment mapping
    [FAILED]
Error: segment-based junction search failed with err =-11
Loading left segment hits...

Thanks a lot for your help,

N.

[Arun]

A fix on seqanswers for this seems to be rebuilding bowtie index. Also, put your fasta file in the same directory where the bowtie index will be built. You'll save the fasta reconstruction step.

[Nicolas Rosewick]

I rebuild it just before the tophat jobs. And on a two sample, tophat finished well .. so it's a strange problem

[Anna]

Hi,

I have the same problem Error: segment-based junction search failed with err =-11 Loading left segment hits... did someone find a solution?

Answer 1

[Sukhi Singh]

There can be lot of reasons, for that, the best bit is to check the respective logs, check in this case the segment_juncs.log which will give you the exact error. Another reason, could be your tmp dir, which might be full, check that as well. Similar posts which might help you post1 & post2. I also tried to discuss and compile a list of other tophat errors here tophat-error-oserror-errno-2-no-such-file-or-directory, which might help in future.

Cheers

[Nicolas Rosewick]

I don't think is the tmp/ dir. I've more than 1TB free on the server. I check in the segment_juncs.log , it seems that tophat can not load 5 chr (only 23 of the 28 chr are loaded) and in the two samples that finished well all the chr are well loaded.

segment_juncs v2.0.4 (3480M)
---------------------------
[samopen] SAM header is present: 28 sequences.
Loading reference sequences...
    Loading Chr10...done
    Loading Chr11...done
    Loading Chr12...done
    Loading Chr13...done
    Loading Chr14...done
    Loading Chr15...done
    Loading Chr16...done
    Loading Chr17...done
    Loading Chr18...done
    Loading Chr19...done
    Loading Chr1...done
    Loading Chr20...done
    Loading Chr21...done
    Loading Chr22...done
    Loading Chr23...done
    Loading Chr24...done
    Loading Chr25...done
    Loading Chr26...done
    Loading Chr2...done
    Loading Chr3...done
    Loading Chr4...done
    Loading Chr5...done
    Loading Chr6...done
>> Performing segment-search:
Loading left segment hits...

[Sukhi Singh]

How you know, head of the log doesn't show that. Also, check the sam file than. Btw, which species you are working on, is it wheat.

[Nicolas Rosewick]

When I check the sam fil, I have only alignment on 23 of the 28 chr... I work on a mixed reference file (human, bovine)

Answer 2

[scchess]

This is caused by insufficient memory. Please check your available RAM.