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.gruening@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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