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How can I get FastQC html report?

I tried to check the quality of Illumina paired-end NGS read with fast QC. I have fast QC installed on ubuntu16:04 OS. 

$ fastqc -vFastQC v0.11.4

$ java -version
openjdk version "1.8.0_91"
OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14)

I tried to run Fastqc with the following command

$fastqc head_a2_plus_b2_ATTCCT_L001_R2_001.fastq

After execution, it generated only the zip file (No html file ) 

head_a2_plus_b2_ATTCCT_L001_R1_001_fastqc.zip

While I was Executing the fast QC command it gives the following messages:

ava.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 head_a2_plus_b2_ATTCCT_L001_R2_001.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 40% complete for head_a2_plus_b2_ATTCCT_L001_R2_001.fastq
Approx 80% complete for head_a2_plus_b2_ATTCCT_L001_R2_001.fastq
Analysis complete for head_a2_plus_b2_ATTCCT_L001_R2_001.fastq
Failed to process file head_a2_plus_b2_ATTCCT_L001_R2_001.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)

Could you please tell me what I did wrong. I also tried to uninstall and then reinstall fastqc with other paramaters like --extract and so on . In each of the cas I only get the zip file which could not be unziped

fastqc ngs fastqc error fastqc report
• 9,004 views • link
updated by EagleEye EagleEye • written by tcf.hcdg tcf.hcdg

It seems the installation is messed up slightly, because fastqc can't find the reference list of adapter sequences. Have you looked in the /etc/fastqc/Configuration directory?

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

It's under

/usr/local/bin/

I chencked the configuration folder it contined the adapter list

tcf@tcf-Dell-Precision-M3800:/usr/local/bin/FastQC/Configuration$ ls
adapter_list.txt  contaminant_list.txt  limits.tx
• 1 views • link
written by tcf.hcdg tcf.hcdg

Its working now: Actually, it was the file permission error. I changed the fastqc file permission in the FASTQC folder and secondly path of the fastqc was missing while I was executing it.

$ chmod 755 fastqc

$ /usr/local/bin/FastQC/fastqc head_a2_plus_b2_ATTCCT_L001_R2_001.fastq.gz
• 1 views • link
written by tcf.hcdg tcf.hcdg

No "installation" should be needed for FastQC. It is odd to see a user program being put under /etc since that directory contains important system related files.

• 1 views • link
written by GenoMax GenoMax

I unzip the downloaded folder and the type 

sudo apt install fastqc

It's under

/usr/local/bin/
• 1 views • link
written by tcf.hcdg tcf.hcdg

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