Hello,
I am trying to use FASTQC to assess the quality of RNA-seq data. I have installed FASTQC using:

    sudo apt-get update
    sudo apt-get install fastqc

and now when i type fastqc -version I get: FastQC v0.11.4. I am using linux ubuntu 16.04 thus java is already installed and when I type java -version I get: 

    openjdk version "1.8.0_131"
    OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11)
    OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)

I have a fastq file (SRR390728_1.fastq). The file is downloaded from the public domain and looks genuine, with the first lines being:

    > @SRR390728.1 1 length=36 CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGC
    > +SRR390728.1 1 length=36 ;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142 @SRR390728.2 2 length=36 AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGT
    > +SRR390728.2 2 length=36 ;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&& @SRR390728.3 3 length=36 CCAGCCTGGCCAACAGAGTGTTACCCCGTTTTTACT
    > +SRR390728.3 3 length=36
    > -;;;8;;;;;;;,*;;';-4,44;,:&,1,4'./&1 @SRR390728.4 4 length=36 ATAAAATCAGGGGTGTTGGAGATGGGATGCCTATTT
    > +SRR390728.4 4 length=36 1;;;;;;,;;4;3;38;8%&,,;)*;1;;,)/%4+,

When I run:

    fastqc --extract  SRR390728_1.fastq 

I obtain:

    java.io.FileNotFoundException: /etc/fastqc/Configuration/adapter_list.txt (No such file or directory)
    	at java.io.FileInputStream.open0(Native Method)
    	at java.io.FileInputStream.open(FileInputStream.java:195)
    	at java.io.FileInputStream.<init>(FileInputStream.java:138)
    	at java.io.FileInputStream.<init>(FileInputStream.java:93)
    	at uk.ac.babraham.FastQC.Modules.AdapterContent.<init>(AdapterContent.java:75)
    	at uk.ac.babraham.FastQC.Modules.ModuleFactory.getStandardModuleList(ModuleFactory.java:37)
    	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:134)
    	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102)
    	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
    Started analysis of SRR390728_1.fastq
    java.io.FileNotFoundException: /etc/fastqc/Configuration/limits.txt (No such file or directory)
    	at java.io.FileInputStream.open0(Native Method)
    	at java.io.FileInputStream.open(FileInputStream.java:195)
    	at java.io.FileInputStream.<init>(FileInputStream.java:138)
    	at java.io.FileInputStream.<init>(FileInputStream.java:93)
    	at uk.ac.babraham.FastQC.Modules.ModuleConfig.readParams(ModuleConfig.java:87)
    	at uk.ac.babraham.FastQC.Modules.ModuleConfig.<clinit>(ModuleConfig.java:35)
    	at uk.ac.babraham.FastQC.Modules.PerTileQualityScores.processSequence(PerTileQualityScores.java:174)
    	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
    	at java.lang.Thread.run(Thread.java:748)
    Approx 5% complete for SRR390728_1.fastq
    Approx 10% complete for SRR390728_1.fastq
    Approx 15% complete for SRR390728_1.fastq
    Approx 20% complete for SRR390728_1.fastq
    Approx 25% complete for SRR390728_1.fastq
    Approx 30% complete for SRR390728_1.fastq
    Approx 35% complete for SRR390728_1.fastq
    Approx 40% complete for SRR390728_1.fastq
    Approx 45% complete for SRR390728_1.fastq
    Approx 50% complete for SRR390728_1.fastq
    Approx 55% complete for SRR390728_1.fastq
    Approx 60% complete for SRR390728_1.fastq
    Approx 65% complete for SRR390728_1.fastq
    Approx 70% complete for SRR390728_1.fastq
    Approx 75% complete for SRR390728_1.fastq
    Approx 80% complete for SRR390728_1.fastq
    Approx 85% complete for SRR390728_1.fastq
    Approx 90% complete for SRR390728_1.fastq
    Approx 95% complete for SRR390728_1.fastq
    Analysis complete for SRR390728_1.fastq
    Failed to process file SRR390728_1.fastq
    java.lang.IllegalArgumentException: No key called gc_sequence:ignore in the config data
    	at uk.ac.babraham.FastQC.Modules.ModuleConfig.getParam(ModuleConfig.java:148)
    	at uk.ac.babraham.FastQC.Modules.PerSequenceGCContent.ignoreInReport(PerSequenceGCContent.java:57)
    	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:331)
    	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
    	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
    	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
    	at java.lang.Thread.run(Thread.java:748)

I obtain a zip file (6.5 kb) that cannot be opened (archive manager gives the error: 'An error occurred while loading the archive'). Same thing if I don't use the '--extract' option; if I use the interactive method, the program gets stuck at 95% processing. 

What went wrong? looks like FASTQC does not like my java distro.

Please note that 'fastqc' is a perl script in /usr/bin/ and in the same folder, 'java' is a link to '/etc/alternatives/java'.

Thank you

The method you used for installing FastQC is not the one recommended by the authors: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt