Lars Nilse lars20070
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| 2018-09-04 18:10:10,792 : DEBUG : main : Node : Virtual Start : 0:54:1 : clean output ports. | |
| 2018-09-04 18:10:10,792 : DEBUG : KNIME-Workflow-Notifier : WorkflowEditor : : : Workflow event triggered: WorkflowEvent [type=NODE_REMOVED;node=0;old=(WFM) Parallel Chunks 0:54 (IDLE);new=null;timestamp=04-Sep-2018 18:10:10] | |
| 2018-09-04 22:16:54,322 : WARN : pool-2-thread-1 : KNIMEApplication$4 : : : Potential deadlock in AWT Event Queue detected. Full thread dump will follow as debug output. | |
| 2018-09-04 22:16:54,322 : WARN : pool-1-thread-1 : KNIMEApplication$3 : : : Potential deadlock in SWT Display thread detected. Full thread dump will follow as debug output. | |
| 2018-09-04 22:16:54,325 : DEBUG : pool-1-thread-1 : KNIMEApplication$3 : : : "AWT-EventQueue-0" Id=2648 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@2d72a840 | |
| at sun.misc.Unsafe.park(Native Method) | |
| - waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@2d72a840 | |
| at java.util.concurrent |
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> | |
| <IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <SearchParameters id="SP_0" db="D:\data\proteome-databases-OpenMS\uniprot_Escherichia-coli_June-2017_canonical-without-isoforms_reviewed_plus_shuffled.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="" enzyme="trypsin" missed_cleavages="1000" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" > | |
| <FixedModification name="Carboxymethyl (C)" /> | |
| <FixedModification name="Dimethyl (N-term)" /> | |
| <FixedModification name="Dimethyl (K)" /> | |
| <UserParam type="string" name="MS:1001211" value=""/> | |
| <UserParam type="string" name="MS:1001256" value=""/> | |
| <UserParam type="string" name="ChargeCarrierMass" value="1.00727649"/> |
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> | |
| <IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <SearchParameters id="SP_0" db="D:\data\proteome-databases-OpenMS\uniprot_Escherichia-coli_June-2017_canonical-without-isoforms_reviewed_plus_shuffled.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="" enzyme="trypsin" missed_cleavages="1000" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" > | |
| <FixedModification name="Carboxymethyl (C)" /> | |
| <FixedModification name="Dimethyl (N-term)" /> | |
| <FixedModification name="Dimethyl (K)" /> | |
| <UserParam type="string" name="MS:1001211" value=""/> | |
| <UserParam type="string" name="MS:1001256" value=""/> | |
| <UserParam type="string" name="ChargeCarrierMass" value="1.00727649"/> |
lars20070
/ CompleteInstallation.sh
Created
December 6, 2017 05:19
contrib and OpenMS build script for Ubuntu 16.04 (LTS)
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| # See documentation at http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/install_linux.html | |
| # build contrib libraries | |
| git clone https://github.com/OpenMS/contrib.git | |
| mkdir contrib-build | |
| cd contrib-build | |
| cmake -DBUILD_TYPE=EIGEN ../contrib | |
| cmake -DBUILD_TYPE=SEQAN ../contrib | |
| cmake -DBUILD_TYPE=WILDMAGIC ../contrib | |
| cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 ../contrib |
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| immz1179:contrib-build lars$ cmake -DBUILD_TYPE=COINOR ../contrib | |
| -- The C compiler identification is AppleClang 9.0.0.9000038 | |
| -- The CXX compiler identification is AppleClang 9.0.0.9000038 | |
| -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc | |
| -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works | |
| -- Detecting C compiler ABI info | |
| -- Detecting C compiler ABI info - done | |
| -- Detecting C compile features | |
| -- Detecting C compile features - done | |
| -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ |
lars20070
/ SILAC_Lys8Arg10_QExactive_20171116.toppas
Created
November 20, 2017 17:11
precursor mass correction
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="25" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="28" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
lars20070
/ TAILS_doubleMediumHeavy_QExactive_20171026.toppas
Created
October 28, 2017 05:43
OpenMS workflow, TAILS protease analysis (double dimethyl labelling, medium and heavy), Thermo Q Exactive, 26/10/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="28" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="40" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
lars20070
/ TAILS_triple_QExactive_20170720.toppas
Created
October 28, 2017 05:39
OpenMS workflow, TAILS protease analysis (triple dimethyl labelling), Thermo Q Exactive, 20/07/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="32" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="50" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
lars20070
/ SILAC_Lys4Arg6_Lys8Arg10_QExactive_20170811.toppas
Created
August 11, 2017 06:09
OpenMS workflow, SILAC Lys4/Arg6 Lys8/Arg10 labelled quantification, Thermo Q Exactive, 11/08/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="40" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="50" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
lars20070
/ SILAC_Lys4Arg6_Lys8Arg10_QExactive_20170723.toppas
Created
July 23, 2017 12:39
OpenMS workflow, SILAC Lys4/Arg6 Lys8/Arg10 labelled quantification, Thermo Q Exactive, 23/07/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="39" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="49" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |