Failed in Fastqc, wiht out final report

Question

[mafer_309]

Hello, i need help about fastqc

I want to analyze fastq.gz files from RNA-seq but after running in terminal after 95% the report file dont works. Fastqc file does not open and it makes only a zip file and not the html report. This is the error :

usuario@ub-hp:~/Escritorio/pruebas$ fastqc MR1VV1SS02_S3_L004_R1_001.fastq.gz 
java.io.FileNotFoundException: /etc/fastqc/Configuration/adapter_list.txt (No existe el archivo o el directorio)
    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 MR1VV1SS02_S3_L004_R1_001.fastq.gz
java.io.FileNotFoundException: /etc/fastqc/Configuration/limits.txt (No existe el archivo o el directorio)
    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 MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 10% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 15% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 20% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 25% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 30% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 35% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 40% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 45% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 50% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 55% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 60% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 65% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 70% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 75% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 80% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 85% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 90% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Approx 95% complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Analysis complete for MR1VV1SS02_S3_L004_R1_001.fastq.gz
Failed to process file MR1VV1SS02_S3_L004_R1_001.fastq.gz
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)

[Pierre Lindenbaum]

there's something wrong in the FASTQC installation:

/etc/fastqc/Configuration/adapter_list.txt

doesn't exist. Check the parameters of fastqc

[Petr Ponomarenko]

I agree that missing adapter_list.txt is strange. Removing it from FastQC results in the same situation as mafer_309 has (at least on my server). Here is an adapter_list.txt for you, mafer_309 :

Illumina Universal Adapter                  AGATCGGAAGAG
Illumina Small RNA Adapter                  ATGGAATTCTCG
Nextera Transposase Sequence                CTGTCTCTTATA

You can put it in Configuration folder in FastQC. It is very strange that you are missing it.

Header of that file describing what it is doing and how to update it:

# This file contains a set of sequence fragments which will be explicitly
# searched against your library.  The reporting will be similar to the 
# Kmer plot, except that every sequence in this list will be shown so 
# you can use this to judge the level of adapter read-through even if those
# adapter sequences aren't picked out by the Kmer module.
#
# Since every sequence here will be analysed and the results plotted it 
# doesn't make any sense to include duplicate sequences, or to add too
# many sequences since your plot will end up a mess.
#
# You can add more sequences to the file by putting one line per entry
# and specifying a name[tab]sequence.  If the contaminant you add is 
# likely to be of use to others please consider sending it to the FastQ
# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/
# or by directly emailing [e-mail] so other users of
# the program can benefit.
#
# For the time being it's going to be easier to interpret this plot if all
# of the sequences provided are the same length, so we've gone with 12bp
# fragments for now.

This is copyed from FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ without permission. I hope it is fine with Simon Andrews and the Bioinformatics Group at the Babraham Institute

[Petr Ponomarenko]

Could you please put here a link to your MR1VV1SS02_S3_L004_R1_001.fastq.gz or at least its last 5%?