Phenyx Troubleshooting

Phenyx troubleshooting

Updated: October, 2008

This page contains troubleshooting information related to the use of the Phenyx Web Interface (PWI). For additional questions please visit the user manual or contact us . In that latter case, please be ready to send us the following information:

1) in case of an access on the vital-it public server or on the secured OnLine Server: login name, job number, description of the problem;

2) in case of a Linux local installation: the log generated by the command line 'phenyx-check-env' (the output will give the pathway where to find the log) and an archive of the failed job

3) in case of a Windows local installation: a short description of your server and the problem, an archive of the failed job (to generate via Management console > Jobs Management > export/browse files: select job ID and 'job directory archive (zip / tar.gz)', click on the 'export' button);

Messages on the Phenyx desktop

no results found

Your submission went through but no match were found. You should double-check your search parameters.

Make sure you have selected the correct peak list format, particularly if you have bypassed the format alert message
If you've used a two-round search, make sure that your second and first round parameters are compatible
Make sure you haven't restricted your search to a taxonomy that doesn't correspond to your data
Try to resubmit your data using looser parameters
Make sure you have selected a scoring adapted to your instrument
Make sure you have submitted MS/MS data (and not PMF or MS data)

If all search parameters are correct, the message may be due to a memory problem. Please check the corresponding stderr.txt file and look for the message: "std::bad_alloc", which confirms a memory problem. (The stderr.txt file can be found in the Management console >Job investigator >stderr:standard error log.) Then try to resubmit your job at a later time.

List of error messages generated on the PWI

These messages appear mainly on the comment line of the Desktop or in the Progression window.

null.taxocxriterion

This message appears when selecting a taxon (Taxonomy list) that does not exist in the selected databank(s). Please check and correct. If you wish to search all taxons, please use "ROOT".

null.aclistcriterion

When selecting "NO_TAXONOMY", Phenyx only searches accession numbers input by the user in the AC List field. Therefore you need to enter AC numbers that exist in the databank you have selected. Please check and correct. If you wish to search all taxons, please use "ROOT".

identification.postprocessing.failed

This message indicates that the perl post-processing experienced a memory problem. Please resubmit your search.

DbSearchExec.OlavEmptySpectraDataException

This message indicates that there is a format problem (maybe mismatched data format)

check the format of your data for any "special" characters

spectraData.conversionError

There is a format error. Please make sure that the data you submitted correspond to one of the following peak list formats: dta (Sequest format), pkl (Micromass format), mgf (Mascot generic format), bdtx (Bruker XML format), mzData (HUPO Proteomics Standards Initiative international XML format), mzXML (Institute for Systems Biology XML format).

Currently this message also appears if you try to submit more than one mzData file : please use the Convert Spectra feature (Management Console > Convert ms/ms peak lists) to convert your files into different formats and resubmit.

Note: this message may also appear in case you try to submit a extensive datafile on the public server and generate an 'out of memory' status. Please contact us.

XabNode.XABChildNodeOutOfRangeException

This message indicates that there is a format problem (little square, raw data, etc.).

system.call.exception

This message indicates that there is a problem linked to the server.

if your data file is very large, or if you've used very loose parameters, there may have been a server timeout. Try to resubmit your data with more stringent parameters to reduce the search area and the calculation time
the server may have been temporarily down. Try to resubmit your job at a later time

mpiDbSearch.OlavBadSubmissionCommand

This error message is linked to the cluster mode. Some processors may be temporarily down. If you get this message, please try to resubmit your data. If not successful, please contact us.

sigtrap.INT

This message appears when you use the "kill job" feature.

killed

This message appears when you use the "kill job" feature.

sigtrap.WINKILL

This message appears when you use the "kill job" feature.

GPException.CannotOpenFile

This message indicates that Phenyx can't open a certain file. It may be a data file or a configuration file. It can be linked to different factors (access authorisation, non-existing file, etc). Please make a copy of the full error message and send it to us.

XmlArborificator.CannotOpenXmlFileException

This message indicates that Phenyx can't open a certain XML file. Please make a copy of the full error message and send it to us.

ModRes.OlavUnknownModif

You may get this message when searching a precompiled database that contains modification annotations with a customized modification, there may be a conflict between the name of the original modification and the modification you've created. Please contact us if you get this error message.

submitJobs.defaut.error

If you get this error message, please send us a copy of the stderr.txt file. This file can be found in the Management Console > Jobs Management > export/browse files: select the job ID and click on the 'browse files' button.

Peptide.OlavModifConflict

This message can appear with version 1.9 or prior versions of Phenyx. Those versions did not allow users to set two simultaneous fixed modifications. Version 2.0 and above allow you to set more than one fixed modification.

Element.OlavUndefinedElementSymbol

This message indicates that there is an update problem with configuration files. Please contact us if you get this error message.

XabNode.XABUnavailableAttribute

This message indicates that there is an update problem with configuration files. Please contact us if you get this error message.

Digestor.Mod2PosFactory_ModifCombinatoryOverflow

You may get this message when searching with amino acid modification set as "variable" and tolerance "none" (each targeted amino acid is modified). Phenyx generates this error message in case of potential "exploding" calculation runtime due to combinatorics issues, particularly when the number of amino acids that can carry a defined modification in a peptide is important. Please resubmit your data with the default tolerance (<=4) for variable modification.

AminoAcidMask.OlavUnknownAminoAcid

You may get this message when searching with customized modification(s) that are not well defined, for example you put a comma between targeted residues ("S,T" instead of "ST" the correct definition) defined in the Residue field of Residue Modifications (Management Console). Please check the customized definitions or contact us.

GenuFlex.OlavInvalidFlexLicenseException

This message indicates that there is a problem with the validity of your license key. Please contact us.

default.rescue.operation

This message may appear if the server was temporarily down during the submission of your data. Please try again, or contact us if recurrent.

unavailable.datafile

This message appears when you try to resubmit a job already archived, that means the datafiles are compressed and not available. Please uncheck the box "Resubmitted Peak List(s)" and try again using the original datafiles.

spectraData.noMsmsPeakList

If you get this error message, please check the content of your datafile: it could be empty or filled with MS1 data (Peptide Mass Fingerprinting (PMF) data). (Please check also the name of your datafile as this message may also appear with strange characters in datafile name.)

mpd.jobfailed

This message appears when there was a problem on a node or an error from the mpd cluster management. Please resubmit the job.

job.limit.exceeded

This message appears when you try to submit a datafile whose the size exceeds the current limit. Please contact us.

error during import

This message appears when you try to import a job that does not match the selected Import option. Please check Import options and try again, or contact us if recurrent.

DBSeq.DBSeqBlockNotAvailableException

This message may appear when submitting on databanks that you have installed as 'root' user, instead of 'phenyx' user (Phenyx local installation). Please follow the Linux post-installation Instructions > Installing Sequence Databases, to check and correct the owner.

Installer Error messages

You get problems installing or checking the Perl.

Please send us the error report by clicking on the "View the technical log".

When trying to install the local version, you get a dialog box: “The magic number did not match.”

This indicates that your download did not complete successfully. Please try to download again.

You get a dialog box during the Perl installation: “ Could not write value to key HKEY..."

This indicates that you don't have enough access on your computer to perform a complete installation. Please restart the installation with administrator rights or click on the "Ignore" button to finish the installation.

Windows XP (Service Pack 2): "The publisher could not be verified. Are you sure you want to run this software?"

This message indicates that we have not been through all Microsoft certifications. You can select Run and proceed.

Windows XP (Service Pack 2): "Windows security alert! To help protect your computer, Windows firewall... Do you want to keep blocking this program? "Perl Command line interpreter""

You must allow perl scripts to run if you wish to see anything happening on your desktop. Choose "unblock" and proceed.

Errors Reporting Procedure

Reporting errors or bugs for a Windows installation

For all problems concerning the Phenyx Windows installation (blank page, java error), please send us

the information contained in the "About" section accessible by right-clicking on the Phenyx icon located at the bottom right corner of your screen (please copy each information line)
the information contained in the "View Logfile..." section accessible by right-clicking on the Phenyx icon located at the bottom right corner of your screen (please select all and copy)
the information contained in the Help>About section of your browser (browser name, version)