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

Question

[leenaehyeon]

tophat2 mapping error

I always use this command and mapping is successfully end.

tophat -o tophat_out_sample -G hg19_genes.gtf --transcriptome-index hg19_transcripts --library-type fr-firststrand hg19 Sample_1_bbduk.fastq Sample_2_bbduk.fastq

But, Today, I got an error message .. and can't make accepted_hits.bam :(

Yesterday mornig, I tried delete python, and Linux-mint system wad down.. But restored. and Data is Okay. in my opinion, some of Program files are deleted in that process.

Most of the files are working properly.(fastqc, bbmap, fastx..etc.. ) cuffdiff & link are deleted :(

But error message pops up tophat2's last mapping process.

Please help me

[2015-10-23 10:04:26] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-10-23 10:04:26] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2015-10-23 10:04:26] Checking for Bowtie index files (transcriptome)..
[2015-10-23 10:04:26] Checking for Bowtie index files (genome)..
[2015-10-23 10:04:26] Checking for reference FASTA file
[2015-10-23 10:04:26] Generating SAM header for /home/ebiogen/Documents/genome/hg19/hg19
[2015-10-23 10:04:47] Reading known junctions from GTF file
[2015-10-23 10:04:50] Preparing reads
     left reads: min. length=20, max. length=92, 20342170 kept reads (3421 discarded)
    right reads: min. length=20, max. length=95, 20343565 kept reads (2026 discarded)
[2015-10-23 10:15:49] Using pre-built transcriptome data..
[2015-10-23 10:15:53] Mapping left_kept_reads to transcriptome hg19_transcripts with Bowtie2
[2015-10-23 11:16:35] Mapping right_kept_reads to transcriptome hg19_transcripts with Bowtie2
[2015-10-23 12:25:52] Resuming TopHat pipeline with unmapped reads
[2015-10-23 12:25:52] Mapping left_kept_reads.m2g_um to genome hg19 with Bowtie2
[2015-10-23 13:08:07] Mapping left_kept_reads.m2g_um_seg1 to genome hg19 with Bowtie2 (1/3)
[2015-10-23 13:14:46] Mapping left_kept_reads.m2g_um_seg2 to genome hg19 with Bowtie2 (2/3)
[2015-10-23 13:21:17] Mapping left_kept_reads.m2g_um_seg3 to genome hg19 with Bowtie2 (3/3)
[2015-10-23 13:29:23] Mapping right_kept_reads.m2g_um to genome hg19 with Bowtie2
[2015-10-23 14:17:41] Mapping right_kept_reads.m2g_um_seg1 to genome hg19 with Bowtie2 (1/4)
[2015-10-23 14:22:46] Mapping right_kept_reads.m2g_um_seg2 to genome hg19 with Bowtie2 (2/4)
[2015-10-23 14:28:05] Mapping right_kept_reads.m2g_um_seg3 to genome hg19 with Bowtie2 (3/4)
[2015-10-23 14:33:39] Mapping right_kept_reads.m2g_um_seg4 to genome hg19 with Bowtie2 (4/4)
[2015-10-23 14:37:05] Searching for junctions via segment mapping
    [FAILED]
Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.54.0: cannot open shared object file: No such file or directory

Answer 1

[h.mon]

segment_juncs is looking for libboost-thread. You may (probably) install it with:

sudo apt-get install libboost-thread1.54.0

The version available at Linux Mint repositories may be different. To investigate the problem further you may issue:

ldd /usr/local/bin/segment_juncs

This will tell you where should be the libboost-threds your executable is looking for.

[5heikki]

Also, always helpful locate X, e.g. locate libboost_thread.so.1.54.0 just to see if it's anywhere..

[leenaehyeon]

OMG. When I tried as you said , the process was successful ! Awsome

Really thank you! Have a nice day!

still I don't know why libboost removed, But It'll work. :))))) Happy to you!