FastQC not making html output report.

Question

[Shahzad]

Dear All I have latest version of Fastqc and java environment. Fastqc file does not open the program and when I run it from terminal it makes only a zip file and not the html report. zip file is also always broken and "An error occurred while loading the archive".

@ubuntu:~$ java -version openjdk version "1.8.0_03-Ubuntu" OpenJDK Runtime Environment (build 1.8.0_03-Ubuntu-8u77-b03-3ubuntu3-b03) OpenJDK 64-Bit Server VM (build 25.03-b03, mixed mode)

[GenoMax]

I assume you are running FastQC in GUI mode? Can you try running it on the command line (I will assume FastQC, Java are in your $PATH otherwise use full path to FastQC)

$ fastqc *.gz -o some_directory_to_store_output

[Shahzad]

I did it as per your instructions but the results are same

laptop@laptop:~/Desktop/NGSdata$ fastqc output.fastq -o '/home/laptop/Desktop/NGSdata/subdir' 
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 output.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:745)
Approx 5% complete for output.fastq
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Approx 95% complete for output.fastq
Analysis complete for output.fastq
Failed to process file output.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:745)

[GenoMax]

Are you using the latest FastQC available?
I am not sure why you decided to put fastqc under /etc (it looks like you must have just moved/copied fastqc perl script to /etc). Can you run fastqc from the original folder (without moving the script out of the FastQC directory)?

Answer 1

[Philipp Bayer]

This seems to be a bug when installing fastqc using apt-get install fastqc on some versions of Ubuntu.

One workaround is to keep the installation like this, download fastqc, and extract the contents of the fastqc zip into /etc/fastqc, then the system-wide fastqc installation will work fine.

Answer 2

[Shahzad]

Thank you for pointing out the mistake. It solved my problem. I installed it using sudo apt install fastqc

this installed a previous version Now I've downloaded the latest version but a simple command did not work. But a little amendment in command after cd to the program directory ./fastqc did the trick. Thanks again.

[yves]

Hi, I have same problem. can you tell me more detail how you solved that please?

[qh.jiang]

This error happened after I update my ubuntu system.... I think maybe that is the reason. Follow the error "java.io.FileNotFoundException......" I have tried to copy the "./Fastqc/fastqc/Configuration" to "/etc/fastqc" , and it worked. Just make sure you have those documents in that directory ~

[Shicheng Guo]

Your solution works, why not put is as the answer, rather than a comments?

[Shahzad]

I wrote the solution "./fastqc" worked for me. If this doesn't solve your problem just paste the error you are getting. I will try to solve it.

[mankolkar]

I copied the 3 individual files seperately into the etc, after creating the fastqc and configuration directories. You have to use sudo mv command

[mankolkar]

Thanks. That worked purrrfectly!!!

Answer 3

[mafer_309]

I get lost about your problem Can you please tell me what did you do different to fix the error.

Thanks u