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: 184.108.40.206 [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.