Hi,

I have encountered the following issue when I try to use FastQC tool in Galaxy. 
 The fastqc file is validated using the fastqvalidator tool and the same files 
have been processed by other tools (i.e bwa) without any complaints about the 
fastqc .  Also, if I ran the fastqc from the command line it gets executed 
without any issue too.

I have updated my galaxy repository in case there is new updates and the FastQC 
version is v0.11.2

Is this something to do with the FastQC wrapper in galaxy?

If it helps, the fastq files are in the file system and I link to them into 
galaxy using the options Link and Fastqqsanger as data type.

Any help will be highly appreciated.
...........
Fatal error: Exit code 1 ()
Failed to process L-20417_S7_L007_R2_001.fastq
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start 
with '@'
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:89)
        at 
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:104)
        at 
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at 
uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:122)
        at 
uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:95)
        at 
uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308)
Traceback (most recent call last):
  File 
"/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py",
 line 162, in <module>
    fastqc_runner.run_fastqc()
  File 
"/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py",
 line 136, in run_fastqc
    self.copy_output_file_to_dataset()
  File 
"/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py",
 line 109, in copy_output_file_to_dataset
    with open(result_file[0], 'rb') as fsrc:
IndexError: list index out of range

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