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#105 hardklor output: crux hardklor different than crux bullseye
If I run crux Bullseye, the intermediate hardklor output is different than the output from crux Hardklor on the same file and same parameters. There are two kinds of differences:
- the crux Bullseye intermediate hardklor output is in an xml format, which is unreadable by the crux Bullseye, so it segfaults when trying to read it. crux Hardklor output is tab-delimited.
- the content of the two files is different.
Here's the crux Bullseye command I use, and its intermediate hardklor.mono.txt file is attached:
/net/gs/vol1/home/alexhu/bin/crux bullseye --parameter-file /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/2013-12-02/bullseye/bullseye.params.txt --overwrite T --output-dir /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/2013-12-02/bullseye/orbiparams /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/ms1/82593_lv_mcx_DDA.ms1 /net/gs/vol1/home/alexhu/proj/crux-projects/2013MouseHeartProteome/data/charged/centroided/82593_lv_mcx_DDA.ms2
Here's the crux Hardklor command I use, and its output is in the folder /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/2013-12-02/crux_hardklor .
/net/gs/vol1/home/alexhu/bin/crux hardklor --parameter-file /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/2013-12-02/bullseye/bullseye.params.txt --overwrite T --output-dir /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/2013-12-02/crux_hardklor --verbosity 100 /net/noble/vol3/user/alexhu/proj/crux-projects/2013MouseHeartProteome/data/ms1/82593_lv_mcx_DDA.ms1
Related
Could you try repeating this with the latest svn version? I am having trouble reproducing this bug on arginine
I SVN updated last week at 11:12, and I have repeated the problem on arginine. What happens for you? This is strange.
I just svn checked-out the latest version of crux and ran the same command on arginine. I get the same problem. Is there anything I can do to help you reproduce it? Or should I work myself to figure out what the problem is?
Kaipo, can you try to reproduce this? Sean can't get it to happen.
Bill
On Mar 20, 2014 5:25 PM, "Alex Hu" alexkhu@users.sf.net wrote:
Related
Issues: #105
Hi guys,
I wasn't able to reproduce this - ran it and the hardklor outputs were the same (crux hardklor on tyrosine, crux bullseye on glutamine).
I have an idea to try and fix this if Alex is still finding this issue occurs for him. We can rewrite the application interface to set the hardklor parameters programmatically rather than by calling hardklor with the parameters set in the command line. Will take some time to implement.
If Kaipo and Sean can't reproduce the problem, then I am OK with pushing
this to post v2.0.
Bill
On Fri, Mar 21, 2014 at 12:23 PM, sjoemac sjoemac@users.sf.net wrote:
Related
Issues: #105