Problem with my reference file

[LouiseT]

Hi everyone
I am getting an error message that I do not understand when I try to annotate my reference file.
The error:

$ bedmap --echo --echo-map-id --delim '\t' Joined_CNVs.bed GeneIDs.bed > ret.bed
dyld: lazy symbol binding failed: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Bioinf/bin/bedmap
  Expected in: /usr/lib/libstdc++.6.dylib

dyld: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Bioinf/bin/bedmap
  Expected in: /usr/lib/libstdc++.6.dylib

Trace/BPT trap: 5

I have narrowed it down to a problem with my Joined_CNVs.bed file as the command and map file work on other reference files. Also when I copy a bit of my reference file into a new file it works. SO something must be wrong with my Jonied_CNV file. I just cant find out what it is.

A section of my reference file:

chr1   19984475   19999707   M3250110011   53.6419   Partition
chr1   19985080   20009737   M3218122111   20.8098   Partition
chr1   47879949   47925846   M3250110011   22.8606   Partition
chr1   53916576   53933856   M3218110001   21.1609   Partition
chr1   54690037   54723713   M3545122114   20.7648   Partition

my map file:

chr1   14362   29370   "WASH7P,NR_024540"
chr1   34611   36081   "FAM138A,NR_026818;FAM138C,NR_026822;FAM138F,NR_026820"
chr1   69090   70008   "OR4F5,NM_001005484"
chr1   323891   328580   "LOC100132062,NR_028325;LOC100132287,NR_028322;LOC100133331,NR_028327"
chr1   367658   368595   "OR4F16,NM_001005277;OR4F29,NM_001005221;OR4F3,NM_001005224"
chr1   566188   566265   "MIR1977,NR_031741"

The output I get when it works on a different reference file:


hr10   35956671   35985781   
chr10   77154078   77201601   "NCRNA00245,NR_024421;NCRNA00245,NR_024422;ZNF503,NM_032772"
chr10   128583729   128604613   "DOCK1,NM_001380;FAM196A,NM_001039762"
chr11   1273671   1502097   "MUC5B,NM_002458";"TOLLIP,NM_019009";"LOC255512,NR_029409";"BRSK2,NM_003957";"CTSD,NM_001909;DUSP8,NM_004420;FAM99A,NR_026643;FAM99B,NR_026642;KRTAP5-1,NM_001005922;KRTAP5-2,NM_001004325;KRTAP5-3,NM_001012708;KRTAP5-4,NM_001012709;KRTAP5-5,NM_001001480;KRTAP5-6,NM_001012416;LOC338651,NR_021489;LOC402778,NM_001170820;MOB2,NM_001172223;MOB2,NM_053005"

Any suggestions to what is going wrong?

Thanks

[AlexReynolds]

Hi Louise,

Sorry to hear you are having difficulties. Can you run your bedmap command with the --ec option and report any error messages, if you see them? Also, can you describe your setup (OS X, Linux, version, system memory, etc.)?

Regards,
Alex

[sjn]

Hi LouiseT,

In addition to what Alex is asking for, can you also run:

file /Bioinf/bin/bedmap

also, can you report which version of bedmap you're using?

/Bioinf/bin/bedmap --help
the version will be near the top of the output.

Thanks,
Shane

[LouiseT]

Hi, Thanks for replying.

if I use --ec I get this:

$ bedmap --echo --ec --echo-map-id --delim '\t' CNVs_3c.bed GeneIDs.bed > BedMap.bed
dyld: lazy symbol binding failed: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Bioinf/bin/bedmap
  Expected in: /usr/lib/libstdc++.6.dylib

dyld: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Bioinf/bin/bedmap
  Expected in: /usr/lib/libstdc++.6.dylib

Trace/BPT trap: 5

(as the command works on other reference files I don't get the reference from / expected in comments)

I am working on a Mac OS X 10.8.2
The bedOps version is v2.0.0 (bedops_macosx_intel_fat-v2.0.0b.tar)

53132-b99690:Tryals lthingholm$ file /Bioinf/bin/bedmap
/Bioinf/bin/bedmap: Mach-O universal binary with 2 architectures
/Bioinf/bin/bedmap (for architecture i386):   Mach-O executable i386
/Bioinf/bin/bedmap (for architecture x86_64):   Mach-O 64-bit executable x86_64

version of bed map:
/Bioinf/bin/bedmap --help
same as Bedops v2.0.0

Think that was all you asked for.
Hope it makes sense !

[sjn]

The same problem occurs for at least some users of 'TopHat' on Mac:  http://seqanswers.com/forums/showthread.php?t=15773

We'll keep searching for a solution.

Shane

[AlexReynolds]

It looks like a core software component (the libstdc++ item you see in the error message) is not being embedded in the OS X binaries we're shipping. As a fallback, bedmap looks for that component elsewhere on your computer and can't find what it needs.

I am researching modifying the developer tools and build process we're using on OS X, so that this piece can get added in properly for the pre-built binaries we ship.

I will follow up once I have some binaries to test out. Sorry for the delay.

[AlexReynolds]

I should probably note that, until I find a fix for this issue, BEDOPS source code is available for download, if you have some experience on the command-line and are willing to do a little bit of preparation to get tools in place.

To start, you'd need Apple Xcode (https://developer.apple.com/xcode/), its command-line tools package (https://developer.apple.com/downloads/index.action) and either MacPorts or Homebrew's distribution of GNU gcc 4.7 or 4.8 (e.g. http://www.macports.org/ports.php?by=name&substr=gcc).

At some point, I'll work out what's needed to compile BEDOPS with clang (Apple's open-source compiler equivalent of gcc), so that MacPorts- or Homebrew-sourced gcc are not required for compiling on OS X. In the meantime, a GNU gcc 4.7 or 4.8 environment is a prerequisite for building BEDOPS on OS X.

Once the development tools are set up, you would basically download the BEDOPS source code, open that folder in Terminal, and run "make; make install". The binaries are placed in the bin directory and can be moved or copied anywhere you'd like that is in your PATH (/usr/local/bin, etc.).

[AlexReynolds]

Thanks for your patience! I have created a beta v2.1 BEDOPS installer for Mac OS X Intel 10.5-10.8, which attempts to address the specific error you have encountered.

If you are interested, I would welcome feedback on its functionality. At this time, the major differences between v2.0 and v2.1 are in conversion scripts — the functionality of other binaries should remain unchanged.

The installer package is available here: https://dl.dropbox.com/u/31495717/BEDOPS%20v2p1p0%20%28beta%29.mpkg.zip

Again, if you try this out and run into any problems, I would appreciate feedback.