Crux-Toolkit / Issues / #255 search-for-xlinks fails to generate q-values

William S Noble - 2015-03-05

labels: --> High priority

assigned_to: sjoemac
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sjoemac - 2015-03-06

Could you try this patch?

issue.255.diff

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- Jeff Howbert - 2015-03-09
  
  Hi Sean,
  
  I don't see an attachment. Do I need to look on SourceForge? Thanks.
  
  Jeff
  
  On Fri, 6 Mar 2015, sjoemac wrote:
  
  Could you try this patch?
  
  Attachment: issue.255.diff (584 Bytes; application/octet-stream)
  
  ** [issues:#255] search-for-xlinks fails to generate q-values**
  
  Status: open
  Milestone: Tide
  Labels: High priority
  Created: Thu Mar 05, 2015 07:37 PM UTC by Jeff Howbert
  Last Updated: Thu Mar 05, 2015 07:43 PM UTC
  Owner: sjoemac
  
  search-for-xlinks fails during its final step of converting match p-values into q-values. The error reported is "Cannot find column distinct matches/spectrum".
  
  These input files will produce the error:
  
  http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
  http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP.fasta
  
  using this command line (with appropriate path modifications):
  
  ./crux_trunk_150223 search-for-xlinks --overwrite T --output-dir CNGP_search-for-xlinks ../data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2 ../data/crosslink/CNGP/CNGP.fasta K:K,nterm:K,nterm:nterm 138.068080
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cruxtoolkit/issues/255/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Issues: ~~#255~~
  
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  - William S Noble - 2015-03-09
    
    Yes, you have to follow the link on the first email in the string. The
    attachment is on sourceforge.
    
    On Mon, Mar 9, 2015 at 4:00 PM, Jeff Howbert howbert@users.sf.net wrote:
    
    Hi Sean,
    
    I don't see an attachment. Do I need to look on SourceForge? Thanks.
    
    Jeff
    
    On Fri, 6 Mar 2015, sjoemac wrote:
    
    Could you try this patch?
    
    Attachment: issue.255.diff (584 Bytes; application/octet-stream)
    
    [issues:#255] http://sourceforge.net/p/cruxtoolkit/issues/255
    search-for-xlinks fails to generate q-values*
    
    Status: open
    Milestone: Tide
    Labels: High priority
    Created: Thu Mar 05, 2015 07:37 PM UTC by Jeff Howbert
    Last Updated: Thu Mar 05, 2015 07:43 PM UTC
    Owner: sjoemac
    
    search-for-xlinks fails during its final step of converting match p-values
    into q-values. The error reported is "Cannot find column distinct
    matches/spectrum".
    
    These input files will produce the error:
    
    http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
    
    http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP.fasta
    
    using this command line (with appropriate path modifications):
    
    ./crux_trunk_150223 search-for-xlinks --overwrite T --output-dir
    CNGP_search-for-xlinks
    ../data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
    ../data/crosslink/CNGP/CNGP.fasta K:K,nterm:K,nterm:nterm 138.068080
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/cruxtoolkit/issues/255/
    
    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/
    
    [issues:#255] http://sourceforge.net/p/cruxtoolkit/issues/255
    search-for-xlinks fails to generate q-values*
    
    Status: open
    Milestone: Tide
    Labels: High priority
    Created: Thu Mar 05, 2015 07:37 PM UTC by Jeff Howbert
    Last Updated: Fri Mar 06, 2015 12:04 AM UTC
    Owner: sjoemac
    
    search-for-xlinks fails during its final step of converting match p-values
    into q-values. The error reported is "Cannot find column distinct
    matches/spectrum".
    
    These input files will produce the error:
    
    http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
    
    http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP.fasta
    
    using this command line (with appropriate path modifications):
    
    ./crux_trunk_150223 search-for-xlinks --overwrite T --output-dir
    CNGP_search-for-xlinks
    ../data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
    ../data/crosslink/CNGP/CNGP.fasta K:K,nterm:K,nterm:nterm 138.068080
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/cruxtoolkit/issues/255/
    
    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/
    
    Related
    
    Issues: ~~#255~~
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Jeff Howbert - 2015-03-10
  
  Hi Sean,
  
  When I applied the patch it changed the name of the column header in search-for-xlinks.target.txt, but search-for-xlinks still failed, with the same error message.
  
  Jeff
  
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  - Jeff Howbert - 2015-03-10
    
    Hi Sean,
    
    Some more information ...
    
    The column header in search-for-xlinks.decoy.txt is unchanged by the patch (still "matches/spectrum") and the error message is in fact slightly different.
    
    Before patch:
    INFO: collapsing targets
    FATAL: Cannot find column distinct matches/spectrum
    
    After patch:
    INFO: collapsing targets
    INFO: collapsing decoys
    FATAL: Cannot find column distinct matches/spectrum
    
    From this I figured out that I need to also change line 179 from "matches/spectrum" to "distinct matches/spectrum".
    
    search-for-xlinks now completes without errors. Committing changes.
    
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Jeff Howbert - 2015-03-10

status: open --> closed
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Jesse Cochrane - 2015-06-19

Hi All -

I am also having this problem, using Crux version 2.1. I've tried both the MacOS precompiled binaries and the Linux precompiled binaries.

Thanks,
Jesse

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- William S Noble - 2015-06-20
  
  Hi Jesse,
  
  We thought we had fixed this problem several months ago. Jeff, who
  resolved the issue, is out of the office today but can presumably look into
  this on Monday. If possible, can you provide a command line and input file
  that causes the problem?
  
  Thanks.
  Bill
  
  On Fri, Jun 19, 2015 at 10:49 AM, Jesse Cochrane <jessecochrane@users.sf.net
  
  wrote:
  
  Hi All -
  
  I am also having this problem, using Crux version 2.1. I've tried both the
  MacOS precompiled binaries and the Linux precompiled binaries.
  
  Thanks,
  Jesse
  
  [issues:#255] http://sourceforge.net/p/cruxtoolkit/issues/255
  search-for-xlinks fails to generate q-values*
  
  Status: closed
  Milestone: Tide
  Labels: High priority
  Created: Thu Mar 05, 2015 07:37 PM UTC by Jeff Howbert
  Last Updated: Tue Mar 10, 2015 12:50 AM UTC
  Owner: sjoemac
  
  search-for-xlinks fails during its final step of converting match p-values
  into q-values. The error reported is "Cannot find column distinct
  matches/spectrum".
  
  These input files will produce the error:
  
  http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
  
  http://noble.gs.washington.edu/~peaklist/proj/data/crosslink/CNGP/CNGP.fasta
  
  using this command line (with appropriate path modifications):
  
  ./crux_trunk_150223 search-for-xlinks --overwrite T --output-dir
  CNGP_search-for-xlinks
  ../data/crosslink/CNGP/CNGP_DSS_trypsin_TCEP_20120110_120110140021_7-26.ms2
  ../data/crosslink/CNGP/CNGP.fasta K:K,nterm:K,nterm:nterm 138.068080
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/cruxtoolkit/issues/255/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Issues: ~~#255~~
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Jeff Howbert - 2015-06-23

I compiled the current Crux trunk, and ran the command line I posted when I originally opened the issue. There were no apparent problems.

Jesse, can you provide the command line and input files that are giving you trouble? Thanks.

Jeff

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search-for-xlinks fails to generate q-values

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#255 search-for-xlinks fails to generate q-values

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