Error with Tophat2 no output

[ae_ucla]

I just ran tophat2 on some data that I previously have alligned. It goes until the last step and I get an error and no output:

[2012-05-03 19:05:31] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-03 19:05:31] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-05-03 19:05:31] Checking for Samtools
Samtools version: 0.1.16.0
[2012-05-03 19:05:31] Checking for Bowtie index files
[2012-05-03 19:05:32] Checking for reference FASTA file
[2012-05-03 19:05:32] Generating SAM header for /scratch0/ref/hg19/bowtie/hg19
format: fastq
quality scale: phred33 (default)
[2012-05-03 19:06:04] Reading known junctions from GTF file
[2012-05-03 19:06:23] Preparing reads
left reads: min. length=100, count=28502086
right reads: min. length=100, count=28482455
[2012-05-03 19:33:03] Creating transcriptome data files..
[2012-05-03 19:34:30] Building Bowtie index from edited_igenome_Homo_Sapiens_GRCh37_genes.fa
[2012-05-03 20:16:30] Mapping left_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 21:23:04] Mapping right_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 22:29:54] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 22:53:32] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 23:17:06] Resuming TopHat pipeline with unmapped reads
[2012-05-03 23:17:58] Mapping left_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-03 23:44:12] Mapping left_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-03 23:49:55] Mapping left_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-03 23:55:08] Mapping left_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:01:12] Mapping left_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:07:12] Mapping right_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-04 00:33:45] Mapping right_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-04 00:39:45] Mapping right_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-04 00:46:05] Mapping right_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:52:44] Mapping right_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:58:14] Retrieving sequences for splices
[2012-05-04 01:01:41] Indexing splices
[2012-05-04 01:04:08] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:06:15] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:08:52] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:11:06] Mapping left_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:13:16] Joining segment hits
[2012-05-04 01:37:45] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:40:01] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:42:15] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:44:31] Mapping right_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:46:38] Joining segment hits
[2012-05-04 02:09:51] Reporting output tracks
Traceback (most recent call last):
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3774, in ?
sys.exit(main())
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3746, in main
params.gff_annotation)
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 2522, in compile_reports
os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
IndexError: list index out of range

I ran on another dataset and the same thing happens.
This is the command I used:
tophat -G $GTF --no-novel-juncs --num-threads 8 -o $DSTDIR/output/tophat200/${BARCODE}_newGTF $REFERENCE $DSTDIR/reads/s_${LANE}_${BARCODE}_1.fastq $DSTDIR/reads/s_${LANE}_${BARCODE}_3.fastq

The only errors I see in the logs are:
reports.log
/share/apps/tophat-2.0.0.Linux_x86_64/tophat_reports: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
long_spanning_reads.segs.log
/share/apps/tophat-2.0.0.Linux_x86_64/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory

These files do in fact exist.

Does any one else have this problem?

[ae_ucla]

It looks like my problem is that I need a higher version of Boost C++ libraries.

[ae_ucla]

I redownloaded tophat2.0.0 today and reran it with no errors. Previously the tophat_reports program at the end (generating final output) would give me the above error. An update fixed it, and it now works.

[csmatyi]

tophat 2.0.9.

Dear all,

I keep getting the following error message when using tophat:

Error running 'long_spanning_reads':/util/opt/tophat/2.0.9/gcc/4.4.7/bin/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

/util/opt/cufflinks/2.1.1/gcc/4.4.7/bin/cufflinks: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

What does this mean?
How do I find out which version of boost that tophat uses?
Also, how can I find out which version of boost long_spanning_reads uses?

Thanks, csmatyi

[NKAkers]

csmatyi,

Have you tried using a precompiled version of tophat rather than building from source? That might be easier than sorting out your boost issue.

[GenoMax]

Dear all,

I keep getting the following error message when using tophat:

Error running 'long_spanning_reads':/util/opt/tophat/2.0.9/gcc/4.4.7/bin/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

/util/opt/cufflinks/2.1.1/gcc/4.4.7/bin/cufflinks: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

What does this mean?
How do I find out which version of boost that tophat uses?
Also, how can I find out which version of boost long_spanning_reads uses?

Thanks, csmatyi

I second NKAkers suggestion of using pre-compiled binaries for linux for TopHat, if feasible. It will save you additional headaches with boost install.

But if you are up for the challenge here is a thread that goes over how to fix some boost library installation problems (look on the last couple of pages, it is a long thread): http://seqanswers.com/forums/showthread.php?t=4058

Post any errors you run into and we can tackle them.