Question: 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.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at uk.ac.babraham.FastQC.Modules.AdapterContent.(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.(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.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at uk.ac.babraham.FastQC.Modules.ModuleConfig.readParams(ModuleConfig.java:87)
at uk.ac.babraham.FastQC.Modules.ModuleConfig.(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.(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

Answer: 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