Hi,

I think it can.  I tried it from command line and it worked.

-----Original Message-----
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Saturday, September 12, 2015 11:19 AM
To: Hakeem Almabrazi; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] FastQC galaxy issue

Hi,

I'm not sure FASTQC can deal with gz files natively.

In the documentation I found they use zcat:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt

So maybe this is your problem?
Bjoern

> Hi Bjoern,
>
> Thank you for your response.  To answer your question, yes I am running the 
> fastqc on a compressed file  (fastq.gz) but not tarfile.  The files are in 
> the file system and I Link them to galaxy but not “Copying” them,  and I 
> think that is the issue of my problem which I am I am trying to debug.
>
> Here is what I sent earlier in regard to that, please let me know if you have 
> any suggestions on how to go about resolving this issue.
>
> …………..
> 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,
>
>
>
> From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
> Sent: Friday, September 11, 2015 4:32 PM
> To: Hakeem Almabrazi; galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] FastQC galaxy issue
>
> Hi,
>
> are you running fastqc on the compressed tarfile? Or is this file unpacked 
> already when you are running fastqc on it?
>
> Thanks,
> Bjoern
> On 10.09.2015 09:39, Hakeem Almabrazi wrote:
> 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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