Searcher.exe failure due to huge LIST file generated during search
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Alice Zhao
Nov 24, 2014, 4:23:17 PM11/24/14
to plink-and-c...@googlegroups.com
I am trying to ID BS3-crosslinked IPMS samples by pLink and I came across the following error while running flow.exe in the command line (actual error is in red at the bottom):
A system error message box popped saying "Searcher.exe has stopped working. A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available." Button: "Close program". After hitting the button, the pop up goes away and nothing else happens.
The ini file is attached to this message. My sample is an IP from human cell lysis and my database is the human proteome. Is there a method to run pLINK without writing the large LIST file? Or predicting how large the LIST file would be, and breaking the file into separate parts? Thanks in advance!
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultConverter" "C:\pLink\EXPERIMENT1results\1.sample\search\vps26_bs3_2mM1x.inter.convert"[info] Protein report initializing...[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...In the load file.In the load file.[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\1.sample\search\1_inter.filter.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\1.sample\search\1_inter.filter.pbuildParse... Running Sample 1 ...Filter ... Running Sample 1 ...Writing ...done!
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\1.sample\search\total_inter.filter.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\1.sample\search\total_inter.filter.pbuildParse... Running Sample 1 ...Filter ... Running Sample 1 ...Writing ...done!
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\1.sample\search\total_inter.combine.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\1.sample\search\total_inter.combine.pbuildParse... Running Sample 1 ...Filter ... Running Sample 1 ...Writing ...done!
C:\pLink\pLink_release>"C:\pLink\pLink_release\PSMAnalysis" "C:\pLink\EXPERIMENT1results\1.sample\search\vps26_bs3_2mM1.inter.psm"[info] Loading PSM configuration information...[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...1 0 1 02 1 1 03 0 2 04 1 2 05 0 3 06 1 3 0[info] Successfully loaded PSM configuration information.[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultConverter" "C:\pLink\EXPERIMENT1results\1.sample\search\vps26_bs3_2mM1.inter.2plabel.convert"[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...[info] Loading database settings ...[info] Loading simple scoring parameters...
[info] Using open flow for crossLinking identification[info] preprocess module for cross-linking open flow : PRE_PROC_XLINK_HCD[info] score cutoff for cross-linking open flow : 3[info] save 500 candidate peptides for cross-linking open flow
[info] loading ion types for cross-linking open flow[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...1.search: Mon Nov 24 03:14:42 2014spectra list in sample 2 are :C:\pLink\EXPERIMENT1\v5\Alice_IP_V5_11072014.mgfStep : Search by SearcherSearcher of C:\pLink\EXPERIMENT1\v5\Alice_IP_V5_11072014.mgfStep : Extract inter-linked spectraFilter of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_qry.proteins.txtStep : Convert to *.pbuild by XLinkResultConverterFilter of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter_qry.proteins.txtStep : Convert to *.pXBuild by XLinkResultConverterConvert of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter_qry.proteins.txtStep : Filter by pBuildFilter of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter.pbuild.txtStep: Filter all by pBuildFilter of C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.filter.pbuildStep: Combine by pBuildFilter of C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.combine.pbuild
Step : Generate PSM file by PSMAnalysisGen PSM file of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.psmStep : Convert to *.plabel by XLinkResultConverterConvert of C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.2plabel.convert
C:\pLink>C:
C:\pLink>cd "C:\pLink\pLink_release\"
C:\pLink\pLink_release>"C:\pLink\pLink_release\Searcher" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.pfind"[info] SearchEngine initialize...[info] Initializing pFind...[info] Reading Parameter File : C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.pfind[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...[info] Read Parameter File Successful[info] Create Thread Pool...[info] Initialization Finished![info] Running...[info] the path of the MS/MS data: C:\pLink\EXPERIMENT1\v5\Alice_IP_V5_11072014.mgf[info] MS/MS data file format: MGF[info] output path: C:\pLink\EXPERIMENT1results\2.sample\search\[info] Start loading Spectra...[info] Count spectra completed.[info] PreProcessing....[info] Searching... Start Time: Mon Nov 24 03:16:44 2014 Time cost: 10.512 Thread0 : 0 / 4000 Total : 0 / 22221
[info] openning database...[info] Searching... Start Time: Mon Nov 24 03:16:44 2014 Time cost: 13.309 Thread0 : 0 / 4000 Total : 0 / 22221
[info] creating the peptide pair list...[info] Searching... Start Time: Mon Nov 24 03:16:44 2014 Time cost: 13.309 Thread0 : 0 / 4000 Total : 0 / 22221
terminate called after throwing an instance of 'std::runtime_error'
what(): at CPepPairContainer::_WriteToFile()() Failed to write. at SearchEngine.cpp::_SearchEngine_Callback() in the function CFlow::Run
This application has requested the Runtime to terminate it in an unusual way.Please contact the application's support team for more information.A system error message box popped saying "Searcher.exe has stopped working. A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available." Button: "Close program". After hitting the button, the pop up goes away and nothing else happens.
I notice that my C: drive is full because of a LIST File (named 1859383336.list) freshly generated in C:/pLink/pLink_release that is >890 GBs.
I think this must have caused the above "failure to write" error.
Back at the command line, I hit enter after the above error message and the following occurs:
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultFilter" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.filter"[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...[info] Protein report initializing...[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...loading from input protein report..In the load file.can't open report file C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_qry.proteins.txterrors occur while loading ..C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_qry.proteins.txt
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultConverter" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.convert"[info] Protein report initializing...[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...In the load file.can't open report file C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter_qry.proteins.txterrors occur while loading ..
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultConverter" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1x.inter.convert"[info] Protein report initializing...[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...In the load file.can't open report file C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter_qry.proteins.txterrors occur while loading ..
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\2.sample\search\1_inter.filter.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\2.sample\search\1_inter.filter.pbuildParse... Running Sample 1 ... at pFindParser::Parse() Cannot access the file: C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter.pbuild.txt
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.filter.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.filter.pbuildParse... Running Sample 1 ... at pFindParser::Parse() Cannot access the file: C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1_inter.pbuild.txt
C:\pLink\pLink_release>"C:\pLink\pLink_release\builder" "C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.combine.pbuild"
################################ pBuild 2.0.0.5# Release date: April 2, 2011###############################
Reading parameters ... Path: C:\pLink\EXPERIMENT1results\2.sample\search\total_inter.combine.pbuildParse... Running Sample 1 ... at pFindParser::Parse() Cannot access the file: C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM_1_inter\vps26_bs3_5mM_1_inter_DataSet1_pfind.txt
C:\pLink\pLink_release>"C:\pLink\pLink_release\PSMAnalysis" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.psm"[info] Loading PSM configuration information...[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...1 0 1 02 1 1 03 0 2 04 1 2 05 0 3 06 1 3 0[info] Successfully loaded PSM configuration information.[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...can't open report file C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM_1_inter\vps26_bs3_5mM_1_inter_DataSet1_pfind.txtEnter.
C:\pLink\pLink_release>"C:\pLink\pLink_release\XLinkResultConverter" "C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM1.inter.2plabel.convert"[info] Loading database settings ...[info] Selected database(s): GST_sequence_small[info] Loading enzyme settings ...[info] Loading PTM settings ...[info] Loading XLink settings ...[info] Loading ion type settings ...[info] Loading workflow settings ...[info] Loading spectra settings ...[info] Loading cluster settings ...[info] Loading meta information...[info] Loading triple peptide parameters...can't open report file C:\pLink\EXPERIMENT1results\2.sample\search\vps26_bs3_5mM_1_inter\vps26_bs3_5mM_1_inter_DataSet1_pfind.txterrors occur while loading ..Failed to run normal search: [Error 2] The system cannot find the file specified: 'C:\\pLink\\EXPERIMENT1results\\2.sample\\search\\vps26_bs3_5mM1_qry.proteins.txt'After I hit enter here, I am back at the command prompt.
The log file shows:
****************************************start time: Fri Nov 14 15:31:51 2014parameter file: pLink.ini
step 0: index directory: C:\pLink\EXPERIMENT1results\0.index last modified time: Fri Nov 14 15:32:35 2014 running time: 80.0 (s) protein sequence number : 79729 search mode : 1------------------------------spectra list in sample 1 are :C:\pLink\EXPERIMENT1\v2\Alice_IP_V2_11072014.mgf
step 1: search directory: C:\pLink\EXPERIMENT1results\1.sample\search last modified time: Mon Nov 24 03:14:42 2014 running time: 819809.2 (s)------------------------------spectra list in sample 2 are :C:\pLink\EXPERIMENT1\v5\Alice_IP_V5_11072014.mgf
step 2: search directory: C:\pLink\EXPERIMENT1results\2.sample\search Failed to run normal search: [Error 2] The system cannot find the file specified: 'C:\\pLink\\EXPERIMENT1results\\2.sample\\search\\vps26_bs3_5mM1_qry.proteins.txt'No reports were generated.
The output path contains:
11/14/2014 03:33 PM <DIR> 0.index
11/14/2014 03:33 PM <DIR> 1.sample
11/24/2014 03:16 AM <DIR> 2.sample
11/24/2014 02:24 PM 914 pLink.log.txt
Inside 1 and 2 sample search directories:
C:\pLink\EXPERIMENT1results>dir 1.sample\search Volume in drive C has no label. Volume Serial Number is B604-D102
Directory of C:\pLink\EXPERIMENT1results\1.sample\search
11/24/2014 03:16 AM <DIR> .11/24/2014 03:16 AM <DIR> ..11/14/2014 03:33 PM 1,029 1_inter.filter.pbuild11/14/2014 03:33 PM 1,053 normal.bat11/24/2014 03:16 AM 13 running_time.txt11/14/2014 03:33 PM 999 total_inter.combine.pbuild11/14/2014 03:33 PM 1,025 total_inter.filter.pbuild11/14/2014 03:33 PM 303 vps26_bs3_2mM1.inter.2plabel.convert11/14/2014 03:33 PM 260 vps26_bs3_2mM1.inter.convert11/14/2014 03:33 PM 521 vps26_bs3_2mM1.inter.filter11/14/2014 03:33 PM 509 vps26_bs3_2mM1.inter.psm11/24/2014 03:16 AM 0 vps26_bs3_2mM1.inter.psm.output11/14/2014 03:33 PM 1,722 vps26_bs3_2mM1.pfind11/14/2014 03:33 PM 261 vps26_bs3_2mM1x.inter.convert11/24/2014 03:15 AM 393,131,766 vps26_bs3_2mM1_inter.pbuild.txt11/24/2014 03:16 AM 147 vps26_bs3_2mM1_inter.plabel11/24/2014 03:15 AM 826,484 vps26_bs3_2mM1_inter.pXBuild11/24/2014 03:14 AM 49,859,456 vps26_bs3_2mM1_inter_qry.proteins.txt11/24/2014 03:14 AM 94,664,666 vps26_bs3_2mM1_qry.proteins.txt11/24/2014 03:15 AM <DIR> vps26_bs3_2mM_1_inter11/24/2014 03:16 AM <DIR> vps26_bs3_2mM_inter11/24/2014 03:16 AM <DIR> vps26_bs3_2mM_inter_combineC:\pLink\EXPERIMENT1results>dir 2.sample\search
Directory of C:\pLink\EXPERIMENT1results\2.sample\search
11/24/2014 02:24 PM <DIR> .11/24/2014 02:24 PM <DIR> ..11/24/2014 03:16 AM 1,029 1_inter.filter.pbuild11/24/2014 03:16 AM 1,053 normal.bat11/24/2014 03:16 AM 999 total_inter.combine.pbuild11/24/2014 03:16 AM 1,025 total_inter.filter.pbuild11/24/2014 03:16 AM 303 vps26_bs3_5mM1.inter.2plabel.convert11/24/2014 03:16 AM 260 vps26_bs3_5mM1.inter.convert11/24/2014 03:16 AM 521 vps26_bs3_5mM1.inter.filter11/24/2014 03:16 AM 509 vps26_bs3_5mM1.inter.psm11/24/2014 02:24 PM 0 vps26_bs3_5mM1.inter.psm.output11/24/2014 03:16 AM 1,717 vps26_bs3_5mM1.pfind11/24/2014 03:16 AM 261 vps26_bs3_5mM1x.inter.convert11/24/2014 02:24 PM <DIR> vps26_bs3_5mM_1_inter11/24/2014 02:24 PM <DIR> vps26_bs3_5mM_inter11/24/2014 02:24 PM <DIR> vps26_bs3_5mM_inter_combineThe ini file is attached to this message. My sample is an IP from human cell lysis and my database is the human proteome. Is there a method to run pLINK without writing the large LIST file? Or predicting how large the LIST file would be, and breaking the file into separate parts? Thanks in advance!
Message has been deleted
Alice Zhao
Dec 1, 2014, 3:41:18 PM12/1/14
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I re-ran the search with one modification: run 1 sample instead of 2 samples. The search ran to completion (I guess?) and generated a report file but it did not find any identification results (#total spectra= 0, #spectra=0, #peptides=0, #proteins=0, #groups=0). A non-informative error was shown in the command line but the program seems to have ignored/bypassed it and proceeded without needing my input:
[info] Loading triple peptide parameters...50NO2_ProteinIDs=val =errors occur while loading ..1.search: Thu Nov 27 06:30:26 2014Step : Copy Index InfoCould someone please help me identify what this error means and how it may have affected my search results?
Despite showing no IDs in report, which I guess is just the intermolecular contacts, I do see expected proteins in the "1.sample/search/" files that contain common and mono-linked results.
I have attached the following from this run:
latest command line messages containing the above mentioned error, log file, ini configuration file, and FDR.
Shengbo Fan
Dec 2, 2014, 10:48:56 PM12/2/14
to plink-and-c...@googlegroups.com
Hi,
It seems that the error is caused due to the large LIST file. That's because an exhausitive mode is used for large database. May try to use open mode instead, add the following line in pLink.ini:
search_mode=1
And this mode will not generate the LIST file. See if that works.
Alice Zhao
Dec 3, 2014, 5:26:26 PM12/3/14
to plink-and-c...@googlegroups.com
Thanks for the informative answer. Just to clarify though, the error due to the LIST file was described in the first post. Is the error in my second post, repeated below, also due to the LIST file? The errors appear to be very different, and I did not notice a LIST file from that run, so I just wanted to confirm:
[info] Loading triple peptide parameters...50NO2_ProteinIDs=val =errors occur while loading ..1.search: Thu Nov 27 06:30:26 2014Step : Copy Index InfoThanks again!
Shengbo Fan
Dec 4, 2014, 8:15:44 AM12/4/14
to plink-and-c...@googlegroups.com
According to the log file, this error is not of big problem, the search should have been finished successfully.
This error happens during the generation of a pLabel file for unknown reason, which is actually used for the annotation part. So it doesn't matter, the results are just correct.
ven...@pw.usda.gov
May 13, 2015, 3:45:24 PM5/13/15
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I am having problems with the Searcher failing in pLink-SS. Has anyone solved this problem?. I receive a Windows error message: Searcher.exe Stopped Working
The diagnostic messages were:
Problem signature:
Problem Event Name: APPCRASH
Application Name: Searcher.exe
Application Version: 0.0.0.0
Application Timestamp: 53c5243b
Fault Module Name: libXLinkPeptideScore.dll
Fault Module Version: 0.0.0.0
Fault Module Timestamp: 53c523da
Exception Code: c0000005
Exception Offset: 00006bd8
OS Version: 6.1.7601.2.1.0.256.48
Locale ID: 1033
Additional Information 1: 0a9e
Additional Information 2: 0a9e372d3b4ad19135b953a78882e789
Additional Information 3: 0a9e
Additional Information 4: 0a9e372d3b4ad19135b953a78882e789
When the Windows message window is closed then in the CMD window the message below appears.
[info] 800000/1664943
Failed to run normal search: [Error 2] The system cannot find the file specified: 'C:\\pLink-SS\\Yecoro rojo-pH6.5-Thermo-pk-1\\Non-Specific\\1.sample\\search\\Yr-pH-6.5-Thermo1_qr
y.proteins.txt'
Traceback (most recent call last):
File "flow.py", line 274, in <module>
File "flow.py", line 141, in main
File "flow.py", line 262, in end_log
ValueError: I/O operation on closed file
c:\pLink-SS>
The diagnostic messages were:
Problem signature:
Problem Event Name: APPCRASH
Application Name: Searcher.exe
Application Version: 0.0.0.0
Application Timestamp: 53c5243b
Fault Module Name: libXLinkPeptideScore.dll
Fault Module Version: 0.0.0.0
Fault Module Timestamp: 53c523da
Exception Code: c0000005
Exception Offset: 00006bd8
OS Version: 6.1.7601.2.1.0.256.48
Locale ID: 1033
Additional Information 1: 0a9e
Additional Information 2: 0a9e372d3b4ad19135b953a78882e789
Additional Information 3: 0a9e
Additional Information 4: 0a9e372d3b4ad19135b953a78882e789
When the Windows message window is closed then in the CMD window the message below appears.
[info] 800000/1664943
Failed to run normal search: [Error 2] The system cannot find the file specified: 'C:\\pLink-SS\\Yecoro rojo-pH6.5-Thermo-pk-1\\Non-Specific\\1.sample\\search\\Yr-pH-6.5-Thermo1_qr
y.proteins.txt'
Traceback (most recent call last):
File "flow.py", line 274, in <module>
File "flow.py", line 141, in main
File "flow.py", line 262, in end_log
ValueError: I/O operation on closed file
c:\pLink-SS>
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