An error occured during fastqc.

Question

[rahul]

Dear All I have install latest version of FastQC and java environment. FastQC unable to complete the run, when I run it from the terminal an error occurred.

~/Desktop/NGS/raw_data$ fastqc -f fastq sample.fastq.gz
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 sample.fastq.gz
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 sample.fastq.gz

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[flogin]

Have you tried this solution? https://github.com/guyleonard/evomics_2017/issues/4

[rahul]

Thank you Flogin. Initially I installed fastqc by using terminal but its dosn't work, so I removed fastqc from APT install and install manually. And after installing manually when I execute to run the sample, its shows error which I mentioned earlier.

Answer 1

[cpad0112]

This is a general problem if you have installed fastqc from ubuntu repos (may be the same with debian and mint as well). Copy the txt files in fastqc repo (https://github.com/s-andrews/FastQC/tree/master/Configuration) into /etc/fastqc/Configuration folder (assuming that you have root/sudo privileges). If system doesn't have such directory, create the directory and copy the files. This should resolve your issue. rk10496mailm

Answer 2

[Arup Ghosh]

Form the error it looks like adapter list is missing. The Configuration folder of FastQC should contain the following files.

$tree /Toolbox/FastQC/Configuration/
/Toolbox/FastQC/Configuration/
├── adapter_list.txt
├── contaminant_list.txt
└── limits.txt

Download FastQC

[rahul]

Thank you Arup for your output.

Answer 3

[lakhujanivijay]

I highly recommend that you start installation using conda

Step#1 - Read this article , optional but highly recommended to read through.

Step#2 - Install miniconda

• download suitable miniconda installer using this link
• install miniconda - sh Miniconda2-latest-Linux-xxx_xx.sh
• activate conda - conda activate

Step#3 - install fastqc

conda install -c bioconda fastqc