Chip-seq - fastqc: zip file doesn't open

Question

[salamandra]

I have an ubuntu 16.04 LTS OS and have installed the software FastQC from the site: http://www.bioinformatics.babraham.ac.uk/projects/download.html.

when I try to open a .fastq file with FastQC as part of a pipeline: fastqc 'path_to_file/file.fastq' a zip folder with the results is produced in the same directory of fastq file, but throws the error: 'An error occurred while loading the archive' when I try to open the file interactively (by typing fastqc in command line and then click File -> Open) it uploads till 95% and then stops.

Could someone please explain what am I doing wrong? Is it related with the installation?

Note: java version is openjdk version "1.8.0_111" OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2ubuntu0.16.04.2-b14) OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)

[GenoMax]

Are you trying to open the "results zip" file in FastQC or the original sequence?

Results zip file is intended for off-line usage e.g. if you want to plot nucleotide distribution using R or some other program. You should only check the sample.html file to view FastQC results in a normal web browser.

[salamandra]

I can't find any file sample.html. Where is it suppose to be?

[GenoMax]

When you run fastqc (e.g. fastqc sample.fq.gz) there should be two result files produced in the same folder (unless you use -o option to put them in a different directory). One file should be sample.zip and other should be sample.html. Are you running fastqc on command line or using the GUI?

[salamandra]

I tried both, with command line, can't get the sample.html file. with GUI loads the input file till 95% only, it doesn't open.

[GenoMax]

It sounds like you are running out of memory. How big is the sequence file and how much memory do you have?

[salamandra]

sequence file is 185,2 MB free memory 130944 KB

[GenoMax]

Both of those numbers sound odd. Have you manged to get FastQC to produce a report before or is this the first time you are using it?

[salamandra]

it's the first time i'm using..

[GenoMax]

Can you try a small test file (this is test data from EBI-ENA ) to see if we can make sure you can get FastQC working right? Don't uncompress the sequence file after you download (it is ~27MB).

Run the analysis on command line fastqc ERR385893_1.fastq.gz.

This should produce

Started analysis of ERR385893_1.fastq.gz
Approx 5% complete for ERR385893_1.fastq.gz
Approx 10% complete for ERR385893_1.fastq.gz
--some lines removed--
Approx 95% complete for ERR385893_1.fastq.gz
Analysis complete for ERR385893_1.fastq.gz

This should not take longer than a few minutes. You should then get two result files. Open the .html file using a browser to see the results.

352K ERR385893_1_fastqc.html
432K ERR385893_1_fastqc.zip
 27M ERR385893_1.fastq.gz

[salamandra]

It didn't work

After the 95% complete it printed:

Approx 95% complete for ERR385893_1.fastq.gz Analysis complete for ERR385893_1.fastq.gz Failed to process file ERR385893_1.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)

[GenoMax]

It looks like you either have an incomplete or corrupt install of FastQC.

Did you download the FastQC v0.11.5 (Win/Linux zip file)? You may want to do this again.

[salamandra]

After re-installing FastQC and running the test sample you gave didnt show an error. But I can't find the file ERR385893_1_fastqc.html anyware. Maybe it didn't produce the file, as it says: "Failed to process file ERR385893_1.fastq.gz"

It printed this: Approx 95% complete for ERR385893_1.fastq.gz Analysis complete for ERR385893_1.fastq.gz Failed to process file ERR385893_1.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)