Author Topic: error messages in wig2bed  (Read 8633 times)

NiamhMR

  • Newbie
  • *
  • Posts: 4
error messages in wig2bed
« on: May 14, 2013, 07:51:01 AM »
Hi,
I am trying to convert a ucsc wig file (which I made using UCSC's BigWigToWig tool) into bed format using your wig2bed tool, but I keep getting the error message:
Non-numeric start coordinate.  See line 6925714 in -.
(remember that chromosome names should not contain spaces.)
but when I look at the lines around this line I don't see any structural issue with my file:
 sed -n '6925710,6925720'p wgEncodeCrgMapabilityAlign100mer.wig
chr16   89924048        89924050        0.0625
chr16   89924050        89924072        1
chr16   89924072        89924074        0.5
chr16   89924074        89924075        0.0384615
chr16   89924075        89924076        0.5
chr16   89924076        89924081        1
chr16   89924081        89924085        0.5
chr16   89924085        89924088        0.333333
chr16   89924088        89924100        0.5
chr16   89924100        89924116        1
chr16   89924116        89924120        0.5

Any idea what is going on?

Thanks,
Niamh

sjn

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #1 on: May 14, 2013, 09:20:43 AM »
Hi Niamh,
Thanks for reporting this.  We've recently made some modification to wig2bed, moving from a C program to a python script for various reasons.  I'd be curious to see if our older version of the program will correctly convert this for you.  Could you please download: https://bedops.googlecode.com/files/bedops_linux_x64-v1.2.5b.tgz and try the wig2bed program there?  It would help us in troubleshooting any current problem (and perhaps allow you to move forward with your needs).  That download contains version 1.2.5 Linux 64-bit binaries.  If you're on a mac, use https://bedops.googlecode.com/files/macosx_intel_fat-v1.2.5b.tgz instead.

Thanks,
Shane

NiamhMR

  • Newbie
  • *
  • Posts: 4
Re: error messages in wig2bed
« Reply #2 on: May 15, 2013, 03:32:39 AM »
Hi Shane,
thanks for the suggestion! The older version worked fine.

Thanks for your help,
Niamh
« Last Edit: May 15, 2013, 03:53:41 AM by NiamhMR »

AlexReynolds

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #3 on: May 15, 2013, 01:01:05 PM »
Hi Niamh,

I am sorry you ran into a bug with this script. We will likely go back to the C-based code for wig2bed in the upcoming v2.2 release, for this and for performance reasons.

In the meantime, would you be willing to post your bigwig and wig files somewhere where I can access them? I'd like to figure out where my script went wrong, and having a repeatable way to break it will help me find the cause.

If they are large files, Dropbox.com offers a free 2GB repository.

In any case, if you have time to offer those files, I'd be grateful.

Regards,
Alex
« Last Edit: May 15, 2013, 01:03:15 PM by AlexReynolds »

NiamhMR

  • Newbie
  • *
  • Posts: 4
Re: error messages in wig2bed
« Reply #4 on: May 16, 2013, 05:41:32 AM »
The bigWig file is from UCSC:
http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign100mer.bw

I converted it to wig format using UCSC's bigWigToWig tool:
bigWigToWig http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign100mer.bw  wgEncodeCrgMapabilityAlign100mer.wig

If there is anything else you need let me know :-)

AlexReynolds

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #5 on: May 22, 2013, 09:23:18 PM »
Hi Niamh,

We have updated BEDOPS to v2.2, which includes Bash-based wrappers to the original C-based wig2bed:

http://bedops.uwencode.org/forum/index.php?topic=49.0

This also includes other fixes. Please feel free to follow up with any feedback, if you run into trouble.

Regards,
Alex

NiamhMR

  • Newbie
  • *
  • Posts: 4
Re: error messages in wig2bed
« Reply #6 on: May 27, 2013, 05:12:51 AM »
That's great, thank you for letting me know.
I found the c version worked really well. I also used your vcf2bed tool last week, which also worked a treat. Thanks for providing these tools  :)

bmartyn

  • Newbie
  • *
  • Posts: 2
Re: error messages in wig2bed
« Reply #7 on: September 17, 2013, 03:28:27 AM »
Hi there,

I have just installed bedops 2.2.0.b via the Mac OS X binary.

I am also struggling with wig2bed. I get the error:
dyld: lazy symbol binding failed: Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
  Referenced from: /usr/local/bin/wig2bed_bin
  Expected in: /usr/lib/libstdc++.6.dylib


Is this some 32 bit/64 bit problem?
I am running OS 10.7.5 on Intel Core 2 Duo

The other bedops scripts I have tried eg sort-bed seem to work fine.

Any help much appreciated.

Thanks, Ben

AlexReynolds

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #8 on: September 17, 2013, 11:26:09 AM »
Hi Ben,

I'm sorry for the difficulties with this.

If you have Apple Developer Tools (e.g. Xcode) installed, please open a Terminal session and run the following two commands:

$ sudo install_name_tool -change /opt/local/lib/libstdc++.6.dylib /Library/Application\ Support/BEDOPS/libstdc++.6.dylib /usr/local/bin/wig2bed_bin

And:

$ sudo install_name_tool -change /opt/local/lib/gcc47/libgcc_s.1.dylib /Library/Application\ Support/BEDOPS/libgcc_s.1.dylib /usr/local/bin/wig2bed_bin

If you don't have Apple Developer Tools/Xcode installed, stay tuned and I'll post a link to a nightly build of BEDOPS 2.3 that includes an updated installer.

Regards,
Alex

AlexReynolds

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #9 on: September 17, 2013, 07:43:19 PM »
We'll have an official release up on the new BEDOPS site soon. For now, I have posted a BEDOPS v2.3 OS X Intel (32/64-bit) installer here:

https://dl.dropboxusercontent.com/u/31495717/BEDOPS%202.3.0.mpkg.zip

If you run this installer and have any further issues with wig2bed or other tools, I would greatly appreciate any feedback.

bmartyn

  • Newbie
  • *
  • Posts: 2
Re: error messages in wig2bed
« Reply #10 on: September 19, 2013, 08:51:49 AM »
Many thanks Alex, your commands did the trick perfectly with Bedops v2.2.

Before installing v2.3 should I remove v2.2? Is there any easy way to do that cleanly and completely?

Thanks again,
Ben

AlexReynolds

  • Administrator
  • Jr. Member
  • *****
  • Posts: 72
Re: error messages in wig2bed
« Reply #11 on: September 19, 2013, 08:46:28 PM »
The installer will take care of that by overwriting old apps and dependencies. I don't have an uninstaller written, although I will document that or write one soon, probably with the v2.3 release.