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Old 11-26-2015, 02:22 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
Default fastqc Exception (error)

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.
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Old 11-27-2015, 03:39 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,961
Default

For reference, also posted (and possibly answered) on Biostars: https://www.biostars.org/p/167555/
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Old 11-27-2015, 04:31 AM   #3
frymor
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Location: Germany

Join Date: May 2010
Posts: 149
Default

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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