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Old 03-12-2013, 09:10 AM   #1
Gus
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Location: Irvine CA, USA

Join Date: Dec 2009
Posts: 29
Exclamation New tophat error? `GLIBCXX_3.4.15' not found during segment-based junction search

So far as this error goes I have not been able to find anyone else complaining about it on the interwebs. What is worse: I just did a whole bunch of tophat runs that finished beautifully on the same cluster with the same settings... well I take that back, I think I used no more than 60 cores on a 64 core node before. This time I used 64 of 64. I am rerunning one job with no more than 60 of 64 to see if that has an effect as it seems to for some other issues.

The full error is:
Code:
[2013-03-11 18:32:44] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-03-11 18:32:44] Checking for Bowtie
                  Bowtie version:        2.0.2.0
[2013-03-11 18:32:44] Checking for Samtools
                Samtools version:        0.1.18.0
[2013-03-11 18:32:44] Checking for Bowtie index files
[2013-03-11 18:32:44] Checking for reference FASTA file
[2013-03-11 18:32:44] Generating SAM header for /bio/dunnw/outside_data/bowtie2_indexes/agambiae.CHROMOSOMES-PEST.AgamP3.renamed
        format:          fastq
        quality scale:   phred33 (default)
[2013-03-11 18:32:46] Reading known junctions from GTF file
[2013-03-11 18:32:47] Preparing reads
         left reads: min. length=50, max. length=50, 71219483 kept reads (12046 discarded)
        right reads: min. length=50, max. length=50, 70981128 kept reads (250401 discarded)
[2013-03-11 19:16:41] Creating transcriptome data files..
[2013-03-11 19:17:30] Building Bowtie index from agambiae.BASEFEATURES_PEST-AgamP3.7.fa
[2013-03-11 19:18:49] Mapping left_kept_reads to transcriptome agambiae.BASEFEATURES_PEST-AgamP3.7 with Bowtie2 
[2013-03-11 22:24:33] Mapping right_kept_reads to transcriptome agambiae.BASEFEATURES_PEST-AgamP3.7 with Bowtie2 
[2013-03-12 01:32:10] Resuming TopHat pipeline with unmapped reads
[2013-03-12 01:32:10] Mapping left_kept_reads.m2g_um to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 
[2013-03-12 02:41:05] Mapping left_kept_reads.m2g_um_seg1 to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 (1/2)
[2013-03-12 03:17:31] Mapping left_kept_reads.m2g_um_seg2 to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 (2/2)
[2013-03-12 03:52:45] Mapping right_kept_reads.m2g_um to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 
[2013-03-12 05:01:57] Mapping right_kept_reads.m2g_um_seg1 to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 (1/2)
[2013-03-12 05:40:34] Mapping right_kept_reads.m2g_um_seg2 to genome agambiae.CHROMOSOMES-PEST.AgamP3.renamed with Bowtie2 (2/2)
[2013-03-12 06:18:58] Searching for junctions via segment mapping
        [FAILED]
Error: segment-based junction search failed with err =1
/data/apps/tophat-2.0.6/bin/segment_juncs: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /data/apps/boost-1.49.0/lib/libboost_thread.so.1.49.0)
The command line was

Code:
tophat --mate-std-dev 25 -G /bio/dunnw/outside_data/vectorbase_data/agambiae/Geneset/agambiae.BASEFEATURES_PEST-AgamP3.7.gtf --library-type fr-unstranded -o /bio/dunnw/data/4mosqs_mg_RNAseq/tophat_Ag_00 -p 64 -r 125 --no-coverage-search /bio/dunnw/outside_data/bowtie2_indexes/agambiae.CHROMOSOMES-PEST.AgamP3.renamed /bio/dunnw/fastQs/mnt/drobo03/pairedFastqs/unfiltered/2011-08-23/1325-AAJ-0011.D04FKACXX_s1_1_illumina12index_1_SL6975.fastq,/bio/dunnw/fastQs/mnt/drobo03/pairedFastqs/unfiltered/2011-08-23/1325-AAJ-0012.D04FKACXX_s1_1_illumina12index_2_SL6976.fastq /bio/dunnw/fastQs/mnt/drobo03/pairedFastqs/unfiltered/2011-08-23/1325-AAJ-0011.D04FKACXX_s1_2_illumina12index_1_SL6975.fastq,/bio/dunnw/fastQs/mnt/drobo03/pairedFastqs/unfiltered/2011-08-23/1325-AAJ-0012.D04FKACXX_s1_2_illumina12index_2_SL6976.fastq
Has anyone else seen this?! Anyone got ideas of how to troubleshoot this one?

Thanks,

Gus
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