How can I get FastQC html report?
0
1
Entering edit mode
5.2 years ago
tcf.hcdg ▴ 70

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 • 6.3k views
ADD COMMENT
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

I unzip the downloaded folder and the type

sudo apt install fastqc

It's under

/usr/local/bin/
ADD REPLY
1
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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
ADD REPLY
1
Entering edit mode

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
ADD REPLY

Login before adding your answer.

Traffic: 2114 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6