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 > > Disclaimer: This email and its attachments may be confidential and are > intended solely for the use of the individual to whom it is addressed. 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