Problem running FastQC

Support Requests
#1

Hi, I am having trouble running FastQC on my data. I thought that it was already installed on my instance, but when I tried to run it I got a message telling me to install it using
sudo apt install fastqc
which I did, and it seemed to be successful. Now when I run fastQC, I get the following message

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 A5_R1cat.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:745)

It then tries to run and produces an empty zip file, and this message

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:745)

I’ve tried installing again, and also tried installing with
brew install fastqc

This is using my GVL at Cardiff. Thanks for any help.

#2

FastQC from aptitude has been broken for ages - the adapter file and some others are missing from the package, as you can see above.

I suggest that you:

  1. Remove the apt version:

sudo apt-get purge fastqc

  1. Logout and login to your instance to reset the PATH

  2. Check that you have fastqc installed from brew

brew install fastqc

  1. Check that you’re using the brew install of fastqc

which fastqc

#3

OK, it works after uninstalling and reinstalling from brew
Thanks.

1 Like
#4

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