Hi everybody, I'm new to the RNA-seq data analysis world and I really need your help.
Just one premise: I have poor experience in coding/programming.
I'm using a Mac Pro (2 x 2.8 GHz Quad-core, 18GB RAM). I've installed SAM tools, Boost 1_55_0, Bowtie 2.2.3 and Tophat-2.0.12 (pre compiled for Mac OSX 64bit). I followed the installation instructions that I found in the corresponding manuals and I tested successfully Bowtie2.
But when I tested Tophat (using the test_data file as suggested in the "getting started" manual), I came across this error:
And this is the long_spanning_reads.segs.log file:
I've read several threads but I couldn't find an answer or a solution.
Could you please help me? I have no idea of what is going on.
Thank you,
Alessandro.
Just one premise: I have poor experience in coding/programming.
I'm using a Mac Pro (2 x 2.8 GHz Quad-core, 18GB RAM). I've installed SAM tools, Boost 1_55_0, Bowtie 2.2.3 and Tophat-2.0.12 (pre compiled for Mac OSX 64bit). I followed the installation instructions that I found in the corresponding manuals and I tested successfully Bowtie2.
But when I tested Tophat (using the test_data file as suggested in the "getting started" manual), I came across this error:
[2014-08-23 14:03:53] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-08-23 14:03:53] Checking for Bowtie
Bowtie version: 2.2.2.0
[2014-08-23 14:03:53] Checking for Samtools
Samtools version: 0.1.16.0
[2014-08-23 14:03:53] Checking for Bowtie index files (genome)..
[2014-08-23 14:03:53] Checking for reference FASTA file
[2014-08-23 14:03:53] Generating SAM header for test_ref
[2014-08-23 14:03:53] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2014-08-23 14:03:53] Mapping left_kept_reads to genome test_ref with Bowtie2
[2014-08-23 14:03:53] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2014-08-23 14:03:53] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2014-08-23 14:03:53] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2014-08-23 14:03:53] Mapping right_kept_reads to genome test_ref with Bowtie2
[2014-08-23 14:03:54] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2014-08-23 14:03:54] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2014-08-23 14:03:54] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2014-08-23 14:03:54] Searching for junctions via segment mapping
[2014-08-23 14:03:54] Retrieving sequences for splices
[2014-08-23 14:03:54] Indexing splices
[2014-08-23 14:03:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2014-08-23 14:03:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2014-08-23 14:03:55] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2014-08-23 14:03:55] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':
-----------------------------------------------
[2014-08-23 14:03:53] Checking for Bowtie
Bowtie version: 2.2.2.0
[2014-08-23 14:03:53] Checking for Samtools
Samtools version: 0.1.16.0
[2014-08-23 14:03:53] Checking for Bowtie index files (genome)..
[2014-08-23 14:03:53] Checking for reference FASTA file
[2014-08-23 14:03:53] Generating SAM header for test_ref
[2014-08-23 14:03:53] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2014-08-23 14:03:53] Mapping left_kept_reads to genome test_ref with Bowtie2
[2014-08-23 14:03:53] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2014-08-23 14:03:53] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2014-08-23 14:03:53] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2014-08-23 14:03:53] Mapping right_kept_reads to genome test_ref with Bowtie2
[2014-08-23 14:03:54] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2014-08-23 14:03:54] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2014-08-23 14:03:54] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2014-08-23 14:03:54] Searching for junctions via segment mapping
[2014-08-23 14:03:54] Retrieving sequences for splices
[2014-08-23 14:03:54] Indexing splices
[2014-08-23 14:03:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2014-08-23 14:03:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2014-08-23 14:03:55] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2014-08-23 14:03:55] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':
long_spanning_reads v2.0.12 (4277)
--------------------------------------------
Opening /dev/null for reading
[samopen] SAM header is present: 1 sequences.
Loading reference sequences...
reference sequences loaded.
Loading junctions...done
Loading deletions...done
Loading insertions...done
dyld: lazy symbol binding failed: Symbol not found: __ZNSt15_List_node_base7_M_hookEPS_
Referenced from: /***/***/***/***/long_spanning_reads
Expected in: /usr/lib/libstdc++.6.dylib
dyld: Symbol not found: __ZNSt15_List_node_base7_M_hookEPS_
Referenced from: /***/***/***/***/long_spanning_reads
Expected in: /usr/lib/libstdc++.6.dylib
--------------------------------------------
Opening /dev/null for reading
[samopen] SAM header is present: 1 sequences.
Loading reference sequences...
reference sequences loaded.
Loading junctions...done
Loading deletions...done
Loading insertions...done
dyld: lazy symbol binding failed: Symbol not found: __ZNSt15_List_node_base7_M_hookEPS_
Referenced from: /***/***/***/***/long_spanning_reads
Expected in: /usr/lib/libstdc++.6.dylib
dyld: Symbol not found: __ZNSt15_List_node_base7_M_hookEPS_
Referenced from: /***/***/***/***/long_spanning_reads
Expected in: /usr/lib/libstdc++.6.dylib
Could you please help me? I have no idea of what is going on.
Thank you,
Alessandro.
Comment