FastQC galaxy issue

classic Classic list List threaded Threaded
6 messages Options
| Threaded
Open this post in threaded view
|

FastQC galaxy issue

Hakeem Almabrazi-2

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. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: FastQC galaxy issue

Hakeem Almabrazi-2

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:[hidden email]] On Behalf Of Hakeem Almabrazi
Sent: Thursday, September 10, 2015 10:40 AM
To: [hidden email]
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

 

Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.

Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: FastQC galaxy issue

Björn Grüning-3
In reply to this post by Hakeem Almabrazi-2
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. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: FastQC galaxy issue

Hakeem Almabrazi-2

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:[hidden email]]
Sent: Friday, September 11, 2015 4:32 PM
To: Hakeem Almabrazi; [hidden email]
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. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/
 
To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 

Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: FastQC galaxy issue

Björn Grüning-3
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:[hidden email]]
> Sent: Friday, September 11, 2015 4:32 PM
> To: Hakeem Almabrazi; [hidden email]
> 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. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
>
>
>
> ___________________________________________________________
>
> Please keep all replies on the list by using "reply all"
>
> in your mail client.  To manage your subscriptions to this
>
> and other Galaxy lists, please use the interface at:
>
>   https://lists.galaxyproject.org/
>
>
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/
>
> Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: FastQC galaxy issue

Hakeem Almabrazi-2
Hi,

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

-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Saturday, September 12, 2015 11:19 AM
To: Hakeem Almabrazi; Bjoern Gruening; [hidden email]
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:[hidden email]]
> Sent: Friday, September 11, 2015 4:32 PM
> To: Hakeem Almabrazi; [hidden email]
> 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. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
>
>
>
> ___________________________________________________________
>
> Please keep all replies on the list by using "reply all"
>
> in your mail client.  To manage your subscriptions to this
>
> and other Galaxy lists, please use the interface at:
>
>   https://lists.galaxyproject.org/
>
>
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/
>
> Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
>
Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/