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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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File input error #377

Closed mavino closed 4 years ago

mavino commented 4 years ago

I am running SearchGUI-3.3.16 with 4 different search engines (X! Tandem, MS-GF+, OMSSA and Comet), my fasta file has around 140,000 entries and my spectrum file is around 60 MB. I am not running this analysis command line. The analysis calls by itself peptideshaker 1.16.42. My computer is an Ubuntu 18. By the moment peptide shaker opens up it throws a file input error: "the end of file was reached unexpectedly. The files seem to be corrupt and cannot be opened. I a file is a copy, make sure it is identical to the original"

This is the derbi.log

Wed Oct 16 11:38:17 EDT 2019:
Booting Derby version The Apache Software Foundation - Apache Derby - 10.10.1.1 - (1458268): instance a816c00e-016d-d538-4373-000032714b78 
on database directory /home/mariano/Downloads/PeptideShaker-1.16.42/resources/matches/Uniprot_2017-9_Exp2_fdr1_0_id with class loader jdk.internal.loader.ClassLoaders$AppClassLoader@1affbebc 
Loaded from file:/home/mariano/Downloads/PeptideShaker-1.16.42/lib/derby-10.10.1.1.jar
java.vendor=Ubuntu
java.runtime.version=11.0.4+11-post-Ubuntu-1ubuntu218.04.3
user.dir=/home/mariano/Downloads/PeptideShaker-1.16.42
os.name=Linux
os.arch=amd64
os.version=4.15.0-65-generic
derby.system.home=null
Database Class Loader started - derby.database.classpath=''
----------------------------------------------------------------
Wed Oct 16 11:45:22 EDT 2019: Shutting down Derby engine
----------------------------------------------------------------
Wed Oct 16 11:45:22 EDT 2019:
Shutting down instance a816c00e-016d-d538-4373-000032714b78 on database directory /home/mariano/Downloads/PeptideShaker-1.16.42/resources/matches/Uniprot_2017-9_Exp2_fdr1_0_id with class loader jdk.internal.loader.ClassLoaders$AppClassLoader@1affbebc

Here is my peptideshaker.log

Wed Oct 16 11:45:24 EDT 2019: PeptideShaker version 1.16.42.
Memory given to the Java virtual machine: 4294967296.
Total amount of memory in the Java virtual machine: 136314880.
Free memory: 69749248.
Java version: 11.0.4.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Ubuntu
java.version: 11.0.4
os.name: Linux
memory: 50.4/136.3
processors available: 12
useCommandThread: false
java.io.OptionalDataException
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1614)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1458)
    at java.base/jdk.internal.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at com.compomics.util.io.SerializationUtils.readObject(SerializationUtils.java:58)
    at com.compomics.util.experiment.io.ExperimentIO.loadExperiment(ExperimentIO.java:44)
    at eu.isas.peptideshaker.fileimport.CpsFileImporter.<init>(CpsFileImporter.java:57)
    at eu.isas.peptideshaker.utils.CpsParent.loadCpsFile(CpsParent.java:205)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI$104.run(PeptideShakerGUI.java:5448)

Would you please help me out... Thank you very much

hbarsnes commented 4 years ago

Hi Mariano,

It indeed seems like your PeptideShaker file has gotten corrupted. Have you tried repeating the process to check whether the error is reproducible? This kind of error may occur if the underlying files are altered during the saving of the PeptideShaker, for example by automatic backup systems or similar.

Can you also share the SearchGUI log? It should reveal if something went wrong during the creation of the PeptideShaker project.

Best regards, Harald

mavino commented 4 years ago

No I was not able to reproduce this error and I do not have that specific log...if happens I will post here again. Thanks a lot.

mavino commented 4 years ago

just happened again: SearchGUI log

makeblastdb command: 
/home/mariano/Downloads/SearchGUI-3.3.16/resources/makeblastdb/linux/linux_64bit/makeblastdb -in human-openprot-r1_3-refprots-grch38.83+grch38.p7+uniprot2017_09_27_mod_concatenated_target_decoy.fasta -dbtype prot 

xtandem command: 
/home/mariano/Downloads/SearchGUI-3.3.16/resources/XTandem/linux/linux_64bit/tandem /home/mariano/Downloads/SearchGUI-3.3.16/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

ms-gf+ command: 
/usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xms128M -Xmx4096M -jar /home/mariano/Downloads/SearchGUI-3.3.16/resources/MS-GF+/MSGFPlus.jar -s /home/mariano/Documents/Roucou/proteogenomic/Exp2_786O_nox_scr.mgf -d /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/human-openprot-r1_3-refprots-grch38.83+grch38.p7+uniprot2017_09_27_mod_concatenated_target_decoy.fasta -o /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/.SearchGUI_temp/Exp2_786O_nox_scr.msgf.mzid -t 5.0ppm -tda 0 -mod /home/mariano/Downloads/SearchGUI-3.3.16/resources/MS-GF+/params/Mods.txt -minCharge 2 -maxCharge 4 -inst 3 -thread 12 -m 3 -e 1 -ntt 2 -protocol 0 -minLength 8 -maxLength 30 -n 10 -addFeatures 0 -ti 0,1 

omssa command: 
/home/mariano/Downloads/SearchGUI-3.3.16/resources/OMSSA/linux/omssacl -w -to 0.02 -te 5.0 -teppm -e 0 -v 1 -zl 2 -zh 4 -zt 3 -ti 1 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hc 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 8 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 119 -mv 120 -d human-openprot-r1_3-refprots-grch38.83+grch38.p7+uniprot2017_09_27_mod_concatenated_target_decoy.fasta -fm /home/mariano/Documents/Roucou/proteogenomic/Exp2_786O_nox_scr.mgf -ox /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/.SearchGUI_temp/Exp2_786O_nox_scr.omx -nt 12 

comet command: 
/home/mariano/Downloads/SearchGUI-3.3.16/resources/Comet/linux/comet.exe /home/mariano/Documents/Roucou/proteogenomic/Exp2_786O_nox_scr.mgf 

PeptideShaker command: 
/usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xms128M -Xmx4096M -cp PeptideShaker-1.16.42.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment RefsProt -sample exp2_fdr1 -replicate 0 -identification_files /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/searchgui_out.zip -spectrum_files /home/mariano/Documents/Roucou/proteogenomic/Exp2_786O_nox_scr.mgf -id_params /home/mariano/.compomics/identification_parameters/RefsProt_exp2_fdr1.par -out /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/PeptideShaker_RefsProt_exp2_fdr1.cpsx -gui 1 

PeptideShaker command: 
/usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xms128M -Xmx4096M -jar PeptideShaker-1.16.42.jar -cps /home/mariano/Documents/Roucou/proteogenomic/RefProts_OpenProt v1.3/PeptideShaker_RefsProt_exp2_fdr1.cpsx

derby.log

----------------------------------------------------------------
Mon Oct 21 11:25:52 EDT 2019:
Booting Derby version The Apache Software Foundation - Apache Derby - 10.10.1.1 - (1458268): instance a816c00e-016d-eeec-b27f-00003afaead0 
on database directory /home/mariano/Downloads/PeptideShaker-1.16.42/resources/matches/RefsProt_exp2_fdr1_0_id with class loader jdk.internal.loader.ClassLoaders$AppClassLoader@1affbebc 
Loaded from file:/home/mariano/Downloads/PeptideShaker-1.16.42/lib/derby-10.10.1.1.jar
java.vendor=Ubuntu
java.runtime.version=11.0.4+11-post-Ubuntu-1ubuntu218.04.3
user.dir=/home/mariano/Downloads/PeptideShaker-1.16.42
os.name=Linux
os.arch=amd64
os.version=4.15.0-65-generic
derby.system.home=null
Database Class Loader started - derby.database.classpath=''
----------------------------------------------------------------
Mon Oct 21 11:27:06 EDT 2019: Shutting down Derby engine
----------------------------------------------------------------
Mon Oct 21 11:27:06 EDT 2019:
Shutting down instance a816c00e-016d-eeec-b27f-00003afaead0 on database directory /home/mariano/Downloads/PeptideShaker-1.16.42/resources/matches/RefsProt_exp2_fdr1_0_id with class loader jdk.internal.loader.ClassLoaders$AppClassLoader@1affbebc 
----------------------------------------------------------------

peptideshaker.log

Mon Oct 21 11:27:08 EDT 2019: PeptideShaker version 1.16.42.
Memory given to the Java virtual machine: 4294967296.
Total amount of memory in the Java virtual machine: 136314880.
Free memory: 117463040.
Java version: 11.0.4.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Ubuntu
java.version: 11.0.4
os.name: Linux
memory: 51.2/136.3
processors available: 12
useCommandThread: false
java.io.OptionalDataException
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1614)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1458)
    at java.base/jdk.internal.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at java.base/java.util.HashMap.readObject(HashMap.java:1460)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1160)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2216)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2355)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2249)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2087)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1594)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:430)
    at com.compomics.util.io.SerializationUtils.readObject(SerializationUtils.java:58)
    at com.compomics.util.experiment.io.ExperimentIO.loadExperiment(ExperimentIO.java:44)
    at eu.isas.peptideshaker.fileimport.CpsFileImporter.<init>(CpsFileImporter.java:57)
    at eu.isas.peptideshaker.utils.CpsParent.loadCpsFile(CpsParent.java:205)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI$104.run(PeptideShakerGUI.java:5448)
mavino commented 4 years ago

So I closed the old and opened a new instance of SearchGUI and everything worked out

hbarsnes commented 4 years ago

I guess the only tip I have is to make sure that you are not having more than one PeptideShaker instances running at the same time. Also, I'd recommend not using OpenJDK if possible.

mavino commented 4 years ago

Unfortunately this error is still happening sporadically even with the newer version SearchGUI-3.3.17, and I am sure i have just one version of PeptideShaker opened, what do you mean when you say do not use OpenJDK?...another crazy thing that happens sporadically is checking for Comet search while the analysis does not actually perform it...the config file for comet stays false...

hbarsnes commented 4 years ago

what do you mean when you say do not use OpenJDK?

It is recommended to use the Oracle version of Java as it is more stable and have less issues than the OpenJDK version. Not sure of that is the problem here, but it could make a difference.

another crazy thing that happens sporadically is checking for Comet search while the analysis does not actually perform it...the config file for comet stays false...

Sounds very strange indeed. Are you running more than one search at the same time from the same SearchGUI jar file? Let me know if you manage to figure out if you do anything different when this happens.

mavino commented 4 years ago

these are the version of java I have on my machine: java-11-openjdk-amd64 jdk1.8.0_202 jre1.8.0_202 I used all of them but I still have the problem...

regarding Comet problem, I have checked 4 different search engines in the same instance...

hbarsnes commented 4 years ago

these are the version of java I have on my machine: java-11-openjdk-amd64 jdk1.8.0_202 jre1.8.0_202 I used all of them but I still have the problem...

Ok. So that is not the problem in this case then. Should hopefully be fixed in the upcoming new release of PeptideShaker, as there we have replaced the database backend. I'll let you know as soon as it is available for testing.

regarding Comet problem, I have checked 4 different search engines in the same instance...

That should not be an issue. Can you tell me which four search engines so that I can try to reprodue the error on my end?

mavino commented 4 years ago

The error is sporadic, it happens once in a while... anyways these are the engines: X! Tandem, MS-GF+, OMSSA and Comet.

Thank you very much for everything

mavino commented 4 years ago

So this is the thing to be more precise I let peptideshaker directly be called by searchgui... so searchgui runs and at the end calls peptideshaker...I get my stuff from it like exporting features then I close peptideshaker, re using the same searchgui that I had open originally... I run the analysis for another sample, peptideshaker opens again and so on. This lasts between 4 or 5 times reusing the same instance of searchgui with 4, 5 different samples, then suddenly while opening peptideshaker I get the file configuration error...

hbarsnes commented 4 years ago

This lasts between 4 or 5 times reusing the same instance of searchgui with 4, 5 different samples, then suddenly while opening peptideshaker I get the file configuration error...

If running that many instances of SearchGUI/PeptideShaker in a row, you may consider using the command lines instead? See https://github.com/compomics/searchgui/wiki/SearchCLI and https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI.

hbarsnes commented 4 years ago

This issue should hopefully be solved in the new beta releases of SearchGUI and PeptideShaker. Please see https://groups.google.com/forum/#!topic/peptide-shaker/1ecY0IyMOBM for more details.

If the issue still exists in the beta releases, please open a new issue at https://github.com/compomics/peptide-shaker-2.0-issue-tracker/issues.

If the issue has been solved, it would also be great of you could let us know by replying to this original issue and letting us know. :)

mavino commented 4 years ago

OK I will test those when I have the opportunity. Thank you very much for everything.