Libboost error while running Tophat alignment job

Question

[rajesh27071992]

Hello All,

I am pretty new to RNA-Seq data analysis and trying to use Tophat for alignment of RNA-Seq reads data. I am getting below error while running the Tophat Alignment job.

[2016-04-11 02:18:26] Beginning TopHat run (v2.1.0)
 -----------------------------------------------
[2016-04-11 02:18:26] Checking for Bowtie
          Bowtie version:    2.2.6.0
[2016-04-11 02:18:26] Checking for Bowtie index files (genome)..
[2016-04-11 02:18:26] Checking for reference FASTA file
    Warning: Could not find FASTA file index/athal.fa
[2016-04-11 02:18:26] Reconstituting reference FASTA file from Bowtie index
  Executing: /home/rajesh/Desktop/NGS_RNA_seq_Griffiths_lab/tools/bam-readcount/bin/bowtie2-2.2.6/bowtie2-inspect index/athal > ./tophat_out/tmp/athal.fa
[2016-04-11 02:18:26] Generating SAM header for index/athal
[2016-04-11 02:18:26] Preparing reads

WARNING: read pairing issues detected (check prep_reads.log) !

 left reads: min. length=50, max. length=50, 57985 kept reads (0 discarded)
 right reads: min. length=50, max. length=50, 57985 kept reads (0 discarded)

[2016-04-11 02:18:27] Mapping left_kept_reads to genome athal with Bowtie2 
[2016-04-11 02:18:30] Mapping left_kept_reads_seg1 to genome athal with Bowtie2 (1/2)
[2016-04-11 02:18:30] Mapping left_kept_reads_seg2 to genome athal with Bowtie2 (2/2)
[2016-04-11 02:18:30] Mapping right_kept_reads to genome athal with Bowtie2 
[2016-04-11 02:18:33] Mapping right_kept_reads_seg1 to genome athal with Bowtie2 (1/2)
[2016-04-11 02:18:33] Mapping right_kept_reads_seg2 to genome athal with Bowtie2 (2/2)
[2016-04-11 02:18:34] Searching for junctions via segment mapping

Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
[FAILED]

Error: segment-based junction search failed with err =127

/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.48.0: cannot open shared object file: No such file or directory

• I can see that the segment_juncs file is present in the usr/local/bin directory.

Below are some of the solutions posted earlier which did not help in my case: 1) I have already tried to export the path in variable LD_LIBRARY_PATH (which doesn’t work). 2) Tried to re-install libboost_thread.so.1.48.0, however, getting the error "Couldn't find any package by regex 'libboost_thread.so.1.48.0"

I would really appreciate if anyone could suggest any possible workaround or provide the solution for this particular error.

Thanks in advance for your time and help.

Answer 1

[jwala]

Some thoughts: - Boost 1.48 is pretty old (on 1.60 now). I would follow install instructions for newest boost, should work and install latest thread library. - Did you compile both tophat and Boost with same compiler on same architecture? I would recompile each to be sure. This can cause the above errors. - Try statically linking, but only if your familiar with how to mess with the linker command in the make file. - Double check that the so file exists, and that the LD_LIBRARY_PATH is well formatted

[rajesh27071992]

Hi Jwala,

Thank you very much for your answer. I appreciate your help.

I did installed Boost 1.60 now. I was trying to compile the Boost library, however, has encountered many new errors along the way. I will try again and hopefully will be successful this time.

Just a thought, is there any simple way to compile the boost libraries and get all the dependencies for tophat in place without going through manual install and compilation?

Thanks..

[jwala]

I would suggest debugging the Boost install. Boost is widely used, and should be installable on any system. It could be that you are using the wrong compiler, or have some other more insidious build issue. Fixing this now will likely save you time in the future.

What system are you trying to build on, and with what compiler?

But... it looks like TopHat has a binary already made. Not sure if its statically linked though, which is what you would need to avoid Boost altogether: https://ccb.jhu.edu/software/tophat/index.shtml