Fastq.gz datatype not recognized on import to data library

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Fastq.gz datatype not recognized on import to data library

Previti
Dear all,

In my ongoing saga concerning our data libraries, I came across another issue after our update from 17.09 to 18.05.
When trying to import fastq.gz files into a data library (linking the files from a user directory), the format is not recognized automatically.

I specifically have to set the data type to fastq.gz in order for it to work at all and even then it sometimes ends up throwing an error (state = error).

Is there anything in particular I need to change to make this work reliably?

Cheers,

Christopher



--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
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Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

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Re: Fastq.gz datatype not recognized on import to data library

Nicola Soranzo-3
Hi Christopher,
can you please submit an issue for this at https://github.com/galaxyproject/galaxy/issues/ with the relevant logs and/or tracebacks?

Cheers,
Nicola

On 03/12/2018 13:33, Previti wrote:
Dear all,

In my ongoing saga concerning our data libraries, I came across another issue after our update from 17.09 to 18.05.
When trying to import fastq.gz files into a data library (linking the files from a user directory), the format is not recognized automatically.

I specifically have to set the data type to fastq.gz in order for it to work at all and even then it sometimes ends up throwing an error (state = error).

Is there anything in particular I need to change to make this work reliably?

Cheers,

Christopher



--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



___________________________________________________________
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Re: Fastq.gz datatype not recognized on import to data library

Previti
Ok, I submitted it, hope somebody can help with this.

Cheers,
Christoper

On 12/3/18 3:20 PM, Nicola Soranzo wrote:
Hi Christopher,
can you please submit an issue for this at https://github.com/galaxyproject/galaxy/issues/ with the relevant logs and/or tracebacks?

Cheers,
Nicola

On 03/12/2018 13:33, Previti wrote:
Dear all,

In my ongoing saga concerning our data libraries, I came across another issue after our update from 17.09 to 18.05.
When trying to import fastq.gz files into a data library (linking the files from a user directory), the format is not recognized automatically.

I specifically have to set the data type to fastq.gz in order for it to work at all and even then it sometimes ends up throwing an error (state = error).

Is there anything in particular I need to change to make this work reliably?

Cheers,

Christopher



--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



___________________________________________________________
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/


___________________________________________________________
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/

--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: Fastq.gz datatype not recognized on import to data library

Peter Cock
Christopher filed this as https://github.com/galaxyproject/galaxy/issues/7068

On Mon, Dec 3, 2018 at 4:01 PM Previti
<[hidden email]> wrote:

>
> Ok, I submitted it, hope somebody can help with this.
>
> Cheers,
> Christoper
>
> On 12/3/18 3:20 PM, Nicola Soranzo wrote:
>
> Hi Christopher,
> can you please submit an issue for this at https://github.com/galaxyproject/galaxy/issues/ with the relevant logs and/or tracebacks?
>
> Cheers,
> Nicola
___________________________________________________________
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