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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