Entering edit mode
7.8 years ago
mafer_309
•
0
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)
there's something wrong in the FASTQC installation:
/etc/fastqc/Configuration/adapter_list.txt
doesn't exist. Check the parameters of fastqc
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 :
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 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
Could you please put here a link to your MR1VV1SS02_S3_L004_R1_001.fastq.gz or at least its last 5%?