extract extra info (logs) from history

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extract extra info (logs) from history

Jochen
Hi,

I would like to use the info (log) HISAT is showing, for another tool.
e.g.:
26781724 reads; of these:
  26781724 (100.00%) were unpaired; of these:
    2445411 (9.13%) aligned 0 times
    20399099 (76.17%) aligned exactly 1 time
    3937214 (14.70%) aligned >1 times
90.87% overall alignment rate
[bam_sort_core] merging from 21 f


Is it possible to access these logs?

Cheers Jochen
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Re: extract extra info (logs) from history

Devon Ryan
There are two alignment summary options in the wrapper that will cause
most/all of that to be written to a history item. They're under
"Summary Options".

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]> wrote:

> Hi,
>
> I would like to use the info (log) HISAT is showing, for another tool.
> e.g.:
> 26781724 reads; of these:
>   26781724 (100.00%) were unpaired; of these:
>     2445411 (9.13%) aligned 0 times
>     20399099 (76.17%) aligned exactly 1 time
>     3937214 (14.70%) aligned >1 times
> 90.87% overall alignment rate
> [bam_sort_core] merging from 21 f
>
>
> Is it possible to access these logs?
>
> Cheers Jochen
> ___________________________________________________________
> 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/
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Re: extract extra info (logs) from history

Jochen
Hi Devon,

do you mean Alignment Summary? How can I access that information and use
it for an other tool.

Cheers Jochen


On 26.04.2018 14:14, Devon Ryan wrote:

> There are two alignment summary options in the wrapper that will cause
> most/all of that to be written to a history item. They're under
> "Summary Options".
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: [hidden email]
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]> wrote:
>> Hi,
>>
>> I would like to use the info (log) HISAT is showing, for another tool.
>> e.g.:
>> 26781724 reads; of these:
>>    26781724 (100.00%) were unpaired; of these:
>>      2445411 (9.13%) aligned 0 times
>>      20399099 (76.17%) aligned exactly 1 time
>>      3937214 (14.70%) aligned >1 times
>> 90.87% overall alignment rate
>> [bam_sort_core] merging from 21 f
>>
>>
>> Is it possible to access these logs?
>>
>> Cheers Jochen
>> ___________________________________________________________
>> 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/

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Re: extract extra info (logs) from history

Langhorst, Brad
Flagstat might be a good choice here…

Brad

> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>
> Hi Devon,
>
> do you mean Alignment Summary? How can I access that information and use it for an other tool.
>
> Cheers Jochen
>
>
> On 26.04.2018 14:14, Devon Ryan wrote:
>> There are two alignment summary options in the wrapper that will cause
>> most/all of that to be written to a history item. They're under
>> "Summary Options".
>>
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: [hidden email]
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]> wrote:
>>> Hi,
>>>
>>> I would like to use the info (log) HISAT is showing, for another tool.
>>> e.g.:
>>> 26781724 reads; of these:
>>>   26781724 (100.00%) were unpaired; of these:
>>>     2445411 (9.13%) aligned 0 times
>>>     20399099 (76.17%) aligned exactly 1 time
>>>     3937214 (14.70%) aligned >1 times
>>> 90.87% overall alignment rate
>>> [bam_sort_core] merging from 21 f
>>>
>>>
>>> Is it possible to access these logs?
>>>
>>> Cheers Jochen
>>> ___________________________________________________________
>>> 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/

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Re: extract extra info (logs) from history

Jochen
That's also an interesting tool. Which gives almost the same result as
in the log file of at HISAT output. I'm not sure why the number of
mapped reads are not 100% identical...

but anyway can someone tell me, or maybe Devon did already, where is the
log info of HISAT saved?

Cheers Jochen


On 02.05.2018 12:37, Langhorst, Brad wrote:

> Flagstat might be a good choice here…
>
> Brad
>
>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>
>> Hi Devon,
>>
>> do you mean Alignment Summary? How can I access that information and use it for an other tool.
>>
>> Cheers Jochen
>>
>>
>> On 26.04.2018 14:14, Devon Ryan wrote:
>>> There are two alignment summary options in the wrapper that will cause
>>> most/all of that to be written to a history item. They're under
>>> "Summary Options".
>>>
>>> Devon
>>> --
>>> Devon Ryan, Ph.D.
>>> Email: [hidden email]
>>> Data Manager/Bioinformatician
>>> Max Planck Institute of Immunobiology and Epigenetics
>>> Stübeweg 51
>>> 79108 Freiburg
>>> Germany
>>>
>>>
>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]> wrote:
>>>> Hi,
>>>>
>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>> e.g.:
>>>> 26781724 reads; of these:
>>>>    26781724 (100.00%) were unpaired; of these:
>>>>      2445411 (9.13%) aligned 0 times
>>>>      20399099 (76.17%) aligned exactly 1 time
>>>>      3937214 (14.70%) aligned >1 times
>>>> 90.87% overall alignment rate
>>>> [bam_sort_core] merging from 21 f
>>>>
>>>>
>>>> Is it possible to access these logs?
>>>>
>>>> Cheers Jochen
>>>> ___________________________________________________________
>>>> 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/

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Re: extract extra info (logs) from history

Devon Ryan
By default the logs are just to stdout. You need to use one of the
options (under "Summary Options" on the version on our instance) if
you want things saved as a history item.

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[hidden email]> wrote:

> That's also an interesting tool. Which gives almost the same result as in
> the log file of at HISAT output. I'm not sure why the number of mapped reads
> are not 100% identical...
>
> but anyway can someone tell me, or maybe Devon did already, where is the log
> info of HISAT saved?
>
> Cheers Jochen
>
>
>
> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>
>> Flagstat might be a good choice here…
>>
>> Brad
>>
>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>
>>> Hi Devon,
>>>
>>> do you mean Alignment Summary? How can I access that information and use
>>> it for an other tool.
>>>
>>> Cheers Jochen
>>>
>>>
>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>
>>>> There are two alignment summary options in the wrapper that will cause
>>>> most/all of that to be written to a history item. They're under
>>>> "Summary Options".
>>>>
>>>> Devon
>>>> --
>>>> Devon Ryan, Ph.D.
>>>> Email: [hidden email]
>>>> Data Manager/Bioinformatician
>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>> Stübeweg 51
>>>> 79108 Freiburg
>>>> Germany
>>>>
>>>>
>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>> e.g.:
>>>>> 26781724 reads; of these:
>>>>>    26781724 (100.00%) were unpaired; of these:
>>>>>      2445411 (9.13%) aligned 0 times
>>>>>      20399099 (76.17%) aligned exactly 1 time
>>>>>      3937214 (14.70%) aligned >1 times
>>>>> 90.87% overall alignment rate
>>>>> [bam_sort_core] merging from 21 f
>>>>>
>>>>>
>>>>> Is it possible to access these logs?
>>>>>
>>>>> Cheers Jochen
>>>>> ___________________________________________________________
>>>>> 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/
>
>
> ___________________________________________________________
> 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/
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: extract extra info (logs) from history

Jochen
Thanks Devon,

I think now I got it ;-). We are running 17.05 I might not have the
"Summary Options" ? I cannot find them...

But maybe I can use the flagstat tool for now.

Cheers Jochen


On 02.05.2018 16:34, Devon Ryan wrote:

> By default the logs are just to stdout. You need to use one of the
> options (under "Summary Options" on the version on our instance) if
> you want things saved as a history item.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: [hidden email]
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[hidden email]> wrote:
>> That's also an interesting tool. Which gives almost the same result as in
>> the log file of at HISAT output. I'm not sure why the number of mapped reads
>> are not 100% identical...
>>
>> but anyway can someone tell me, or maybe Devon did already, where is the log
>> info of HISAT saved?
>>
>> Cheers Jochen
>>
>>
>>
>> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>> Flagstat might be a good choice here…
>>>
>>> Brad
>>>
>>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>>
>>>> Hi Devon,
>>>>
>>>> do you mean Alignment Summary? How can I access that information and use
>>>> it for an other tool.
>>>>
>>>> Cheers Jochen
>>>>
>>>>
>>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>> There are two alignment summary options in the wrapper that will cause
>>>>> most/all of that to be written to a history item. They're under
>>>>> "Summary Options".
>>>>>
>>>>> Devon
>>>>> --
>>>>> Devon Ryan, Ph.D.
>>>>> Email: [hidden email]
>>>>> Data Manager/Bioinformatician
>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>> Stübeweg 51
>>>>> 79108 Freiburg
>>>>> Germany
>>>>>
>>>>>
>>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>>> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>>> e.g.:
>>>>>> 26781724 reads; of these:
>>>>>>     26781724 (100.00%) were unpaired; of these:
>>>>>>       2445411 (9.13%) aligned 0 times
>>>>>>       20399099 (76.17%) aligned exactly 1 time
>>>>>>       3937214 (14.70%) aligned >1 times
>>>>>> 90.87% overall alignment rate
>>>>>> [bam_sort_core] merging from 21 f
>>>>>>
>>>>>>
>>>>>> Is it possible to access these logs?
>>>>>>
>>>>>> Cheers Jochen
>>>>>> ___________________________________________________________
>>>>>> 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/
>>
>> ___________________________________________________________
>> 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/

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Re: extract extra info (logs) from history

Devon Ryan-2
Sounds like a good excuse to upgrade :)

Sent from my iPhone

> On 2. May 2018, at 16:40, Jochen Bick <[hidden email]> wrote:
>
> Thanks Devon,
>
> I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them...
>
> But maybe I can use the flagstat tool for now.
>
> Cheers Jochen
>
>
>> On 02.05.2018 16:34, Devon Ryan wrote:
>> By default the logs are just to stdout. You need to use one of the
>> options (under "Summary Options" on the version on our instance) if
>> you want things saved as a history item.
>>
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: [hidden email]
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>>> On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[hidden email]> wrote:
>>> That's also an interesting tool. Which gives almost the same result as in
>>> the log file of at HISAT output. I'm not sure why the number of mapped reads
>>> are not 100% identical...
>>>
>>> but anyway can someone tell me, or maybe Devon did already, where is the log
>>> info of HISAT saved?
>>>
>>> Cheers Jochen
>>>
>>>
>>>
>>>> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>>> Flagstat might be a good choice here…
>>>>
>>>> Brad
>>>>
>>>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>>>
>>>>> Hi Devon,
>>>>>
>>>>> do you mean Alignment Summary? How can I access that information and use
>>>>> it for an other tool.
>>>>>
>>>>> Cheers Jochen
>>>>>
>>>>>
>>>>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>>> There are two alignment summary options in the wrapper that will cause
>>>>>> most/all of that to be written to a history item. They're under
>>>>>> "Summary Options".
>>>>>>
>>>>>> Devon
>>>>>> --
>>>>>> Devon Ryan, Ph.D.
>>>>>> Email: [hidden email]
>>>>>> Data Manager/Bioinformatician
>>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>>> Stübeweg 51
>>>>>> 79108 Freiburg
>>>>>> Germany
>>>>>>
>>>>>>
>>>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>>>> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>>>> e.g.:
>>>>>>> 26781724 reads; of these:
>>>>>>>    26781724 (100.00%) were unpaired; of these:
>>>>>>>      2445411 (9.13%) aligned 0 times
>>>>>>>      20399099 (76.17%) aligned exactly 1 time
>>>>>>>      3937214 (14.70%) aligned >1 times
>>>>>>> 90.87% overall alignment rate
>>>>>>> [bam_sort_core] merging from 21 f
>>>>>>>
>>>>>>>
>>>>>>> Is it possible to access these logs?
>>>>>>>
>>>>>>> Cheers Jochen
>>>>>>> ___________________________________________________________
>>>>>>> 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/
>>>
>>> ___________________________________________________________
>>> 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/
>
___________________________________________________________
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and other Galaxy lists, please use the interface at:
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