fastqc Exception (error)

frymor

Senior Member

Join Date: May 2010
Posts: 151

fastqc Exception (error)

11-26-2015, 03:22 AM

Hi,

I am running the fastqc (v0.11.4) on Ubuntu 14.04.3 LTS.
I have four fastq files (two pairs of paired-end reads samples). They are AFAIK from old solexa machines in sanger format
somehow when I am trying to fastq the _1 files I get the following error message:

Code:

fastqc -t 12 -o ../Results/1c3c603f-29ac-4263-851d-b19f9ce4cfb0/fastqcResults/ 61627AAXX_1_1.fastq.gz 
Started analysis of 61627AAXX_1_1.fastq.gz
Exception in thread "Thread-1" java.lang.IllegalArgumentException: Unexpected cs char C
        at uk.ac.babraham.FastQC.Sequence.FastQFile.convertColorspaceToBases(FastQFile.java:334)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:191)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
        at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
        at java.lang.Thread.run(Thread.java:745)

than nothing happens.
When I am using the same command for the _2 files, it works fine.

Code:

fastqc -t 12 -o ../Results/1c3c603f-29ac-4263-851d-b19f9ce4cfb0/fastqcResults/ 61627AAXX_1_2.fastq.gz 
Started analysis of 61627AAXX_1_2.fastq.gz
Approx 5% complete for 61627AAXX_1_2.fastq.gz
...

I can't see any differences in the format of the two files.

the header of the two files from one of the pairs looks like that:

Code:

zcat 61GAFAAXX_1_1.fastq.gz | head -n 12
@SOLEXA12_1:1:1:990:4777/1 1:Y:0:0
..................................................
+
##################################################
@SOLEXA12_1:1:1:990:11674/1 1:Y:0:0
..................................................
+
##################################################
@SOLEXA12_1:1:1:990:17662/1 1:Y:0:0
..................................................
+
##################################################

and

Code:

zcat 61GAFAAXX_1_2.fastq.gz | head -n 12
@SOLEXA12_1:1:1:990:4777/2 2:Y:0:0
..................................................
+
##################################################
@SOLEXA12_1:1:1:990:11674/2 2:Y:0:0
..................................................
+
##################################################
@SOLEXA12_1:1:1:990:17662/2 2:Y:0:0
..................................................
+
##################################################

Any ideas, why I can't run the _1 files?

thanks
Assa

P.S.
When I am running the SolexaQA++ tool, I can read all the four files without difficulties.

Tags: exception, fastqc, java

GenoMax

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Join Date: Feb 2008

Posts: 7142
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#2

11-27-2015, 04:39 AM

For reference, also posted (and possibly answered) on Biostars: https://www.biostars.org/p/167555/
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frymor

Senior Member

Join Date: May 2010

Posts: 151
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#3

11-27-2015, 05:31 AM

sorry about spamming the forum. I have wanted to delete the entries, but couldn't find any way to do so.
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