Hi again,

After struggling with this issue for few days and exhausted all my options, the 
only thing that was left was to use the "Copy the file into galaxy" instead of 
"Link files into Galaxy" in the loading page.  It took while to copy but after 
it was done, I noticed the file was decompressed and it size was  (240 GB) 
instead of the 30GB.

I re-ran the FastQC tool and it worked.  I am not sure if this is a bug in the 
copying/linking part or at the FastQC wrapper.

Has anyone encountered this issue?  Can anyone try to link a fastq file and run 
the FastQC to confirm what I am seeing?

It is very important to us that we link the fastq files instead of copying them 
into galaxy.

I appreciate any feedback.

Regards,

Hakeem

From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Hakeem Almabrazi
Sent: Thursday, September 10, 2015 10:40 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] FastQC galaxy issue

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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