read_bits64 error when loading large genomes/data into trackster

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read_bits64 error when loading large genomes/data into trackster

Raj Ayyampalayam
Hello,

I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) 
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) 
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) 
  File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) 
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) 
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) 
AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' 

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
How do I get the fixed code into my galaxy instance?

Thanks,
-Raj



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Re: read_bits64 error when loading large genomes/data into trackster

Jeremy Goecks-4
Would it be possible that you have an old copy of the bx-python egg? You should have bx-python 0.7.1  

If you check your eggs directory and you see version 0.7.1, then there may be something wrong with bx-python. In this case, please upload your build and bam to our public server and try again; if it fails on our public server, share the datasets with me and I'll take a look. 

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <[hidden email]> wrote:

Hello,

I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) 
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) 
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) 
  File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) 
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) 
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) 
AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' 

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


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in your mail client.  To manage your subscriptions to this
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Re: read_bits64 error when loading large genomes/data into trackster

Raj Ayyampalayam
I checked the version of bx-python egg and confirmed that it is
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.

I will upload the dataset to the public server and try it over there
and report.

Thanks,
-Raj

On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:

> Would it be possible that you have an old copy of the bx-python egg?
> You should have bx-python 0.7.1
>
> If you check your eggs directory and you see version 0.7.1, then there
> may be something wrong with bx-python. In this case, please upload
> your build and bam to our public server and try again; if it fails on
> our public server, share the datasets with me and I'll take a look.
>
> Thanks,
> J.
>
> --
> Jeremy Goecks
> Assistant Professor, Computational Biology Institute
> George Washington University
>
>
>
> On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hello,
>>
>> I am trying to visualize a large genome (Large number of scaffolds)
>> and a large (bam file) in trackster on our local galaxy instance
>> (running release_2014.02.10).
>> When ever I try to do the above I see the following error in the logs:
>>
>>   File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
>> (lib/bx/bbi/bbi_file.c:5596)
>>   File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
>> (lib/bx/bbi/bbi_file.c:5210)
>>   File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
>> (lib/bx/bbi/bbi_file.c:4475)
>>   File "bbi_file.pyx", line 248, in
>> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
>> (lib/bx/bbi/bbi_file.c:5656)
>>   File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
>> (lib/bx/bbi/bpt_file.c:1388)
>>   File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
>> (lib/bx/bbi/bpt_file.c:1154)
>> AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64'
>>
>> Trackster works OK when I load smaller data sets.
>>
>> It seems that there was a fix for this in bx-python code, as per mail
>> from Jeremy
>> (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
>> How do I get the fixed code into my galaxy instance?
>>
>> Thanks,
>> -Raj
>>
>>
>> ___________________________________________________________
>> 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:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>


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in your mail client.  To manage your subscriptions to this
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Re: read_bits64 error when loading large genomes/data into trackster

Raj Ayyampalayam
Jeremy,

I uploaded my dataset to the main galaxy site and the visualization
failed.
Here is the link to the history:
https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
I used the same genome and a cufflinks gtf file instead of the bam file
(Bam is too big to load).

I am seeing the same problem on both main and my local galaxy instances
(local is tracking latest galaxy-dist).

Thanks,
-Raj


On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:

> I checked the version of bx-python egg and confirmed that it is
> bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.
>
> I will upload the dataset to the public server and try it over there
> and report.
>
> Thanks,
> -Raj
>
> On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:
>> Would it be possible that you have an old copy of the bx-python egg?
>> You should have bx-python 0.7.1
>>
>> If you check your eggs directory and you see version 0.7.1, then there
>> may be something wrong with bx-python. In this case, please upload
>> your build and bam to our public server and try again; if it fails on
>> our public server, share the datasets with me and I'll take a look.
>>
>> Thanks,
>> J.
>>
>> --
>> Jeremy Goecks
>> Assistant Professor, Computational Biology Institute
>> George Washington University
>>
>>
>>
>> On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>> Hello,
>>>
>>> I am trying to visualize a large genome (Large number of scaffolds)
>>> and a large (bam file) in trackster on our local galaxy instance
>>> (running release_2014.02.10).
>>> When ever I try to do the above I see the following error in the logs:
>>>
>>>   File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
>>> (lib/bx/bbi/bbi_file.c:5596)
>>>   File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
>>> (lib/bx/bbi/bbi_file.c:5210)
>>>   File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
>>> (lib/bx/bbi/bbi_file.c:4475)
>>>   File "bbi_file.pyx", line 248, in
>>> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
>>> (lib/bx/bbi/bbi_file.c:5656)
>>>   File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
>>> (lib/bx/bbi/bpt_file.c:1388)
>>>   File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
>>> (lib/bx/bbi/bpt_file.c:1154)
>>> AttributeError: 'BinaryFileReader' object has no attribute
>>> 'read_bits64'
>>>
>>> Trackster works OK when I load smaller data sets.
>>>
>>> It seems that there was a fix for this in bx-python code, as per mail
>>> from Jeremy
>>> (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
>>>
>>> How do I get the fixed code into my galaxy instance?
>>>
>>> Thanks,
>>> -Raj
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>> http://lists.bx.psu.edu/
>>>
>>> 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:
>  http://lists.bx.psu.edu/
>
> 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:
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Re: read_bits64 error when loading large genomes/data into trackster

Jeremy Goecks-4
Hi Raj,

Thanks for sharing your datasets. This issue should be fixed as of this commit in -central:

https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3

Best,
J.

--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University



On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam <[hidden email]> wrote:

Jeremy,

I uploaded my dataset to the main galaxy site and the visualization failed.
Here is the link to the history: https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
I used the same genome and a cufflinks gtf file instead of the bam file (Bam is too big to load).

I am seeing the same problem on both main and my local galaxy instances (local is tracking latest galaxy-dist).

Thanks,
-Raj


On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:
I checked the version of bx-python egg and confirmed that it is
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.

I will upload the dataset to the public server and try it over there
and report.

Thanks,
-Raj

On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:
Would it be possible that you have an old copy of the bx-python egg?
You should have bx-python 0.7.1

If you check your eggs directory and you see version 0.7.1, then there
may be something wrong with bx-python. In this case, please upload
your build and bam to our public server and try again; if it fails on
our public server, share the datasets with me and I'll take a look.

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <[hidden email]
<[hidden email]>> wrote:

Hello,

I am trying to visualize a large genome (Large number of scaffolds)
and a large (bam file) in trackster on our local galaxy instance
(running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

 File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5596)
 File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5210)
 File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
(lib/bx/bbi/bbi_file.c:4475)
 File "bbi_file.pyx", line 248, in
bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
(lib/bx/bbi/bbi_file.c:5656)
 File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
(lib/bx/bbi/bpt_file.c:1388)
 File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
(lib/bx/bbi/bpt_file.c:1154)
AttributeError: 'BinaryFileReader' object has no attribute
'read_bits64'

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail
from Jeremy
(http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).

How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


___________________________________________________________
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:
http://lists.bx.psu.edu/

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:
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To search Galaxy mailing lists use the unified search at:
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Re: read_bits64 error when loading large genomes/data into trackster

Raj Ayyampalayam
Thanks Jeremy.

-Raj

On Wednesday, April 16, 2014 9:32:23 AM, Jeremy Goecks wrote:

> Hi Raj,
>
> Thanks for sharing your datasets. This issue should be fixed as of
> this commit in -central:
>
> https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3
>
> Best,
> J.
>
> --
> Jeremy Goecks
> Assistant Professor of Computational Biology
> George Washington University
>
>
>
> On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Jeremy,
>>
>> I uploaded my dataset to the main galaxy site and the visualization
>> failed.
>> Here is the link to the history:
>> https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
>> I used the same genome and a cufflinks gtf file instead of the bam
>> file (Bam is too big to load).
>>
>> I am seeing the same problem on both main and my local galaxy
>> instances (local is tracking latest galaxy-dist).
>>
>> Thanks,
>> -Raj
>>
>>
>> On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:
>>> I checked the version of bx-python egg and confirmed that it is
>>> bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.
>>>
>>> I will upload the dataset to the public server and try it over there
>>> and report.
>>>
>>> Thanks,
>>> -Raj
>>>
>>> On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:
>>>> Would it be possible that you have an old copy of the bx-python egg?
>>>> You should have bx-python 0.7.1
>>>>
>>>> If you check your eggs directory and you see version 0.7.1, then there
>>>> may be something wrong with bx-python. In this case, please upload
>>>> your build and bam to our public server and try again; if it fails on
>>>> our public server, share the datasets with me and I'll take a look.
>>>>
>>>> Thanks,
>>>> J.
>>>>
>>>> --
>>>> Jeremy Goecks
>>>> Assistant Professor, Computational Biology Institute
>>>> George Washington University
>>>>
>>>>
>>>>
>>>> On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <[hidden email]
>>>> <mailto:[hidden email]>
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to visualize a large genome (Large number of scaffolds)
>>>>> and a large (bam file) in trackster on our local galaxy instance
>>>>> (running release_2014.02.10).
>>>>> When ever I try to do the above I see the following error in the logs:
>>>>>
>>>>>  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
>>>>> (lib/bx/bbi/bbi_file.c:5596)
>>>>>  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
>>>>> (lib/bx/bbi/bbi_file.c:5210)
>>>>>  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
>>>>> (lib/bx/bbi/bbi_file.c:4475)
>>>>>  File "bbi_file.pyx", line 248, in
>>>>> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
>>>>> (lib/bx/bbi/bbi_file.c:5656)
>>>>>  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
>>>>> (lib/bx/bbi/bpt_file.c:1388)
>>>>>  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
>>>>> (lib/bx/bbi/bpt_file.c:1154)
>>>>> AttributeError: 'BinaryFileReader' object has no attribute
>>>>> 'read_bits64'
>>>>>
>>>>> Trackster works OK when I load smaller data sets.
>>>>>
>>>>> It seems that there was a fix for this in bx-python code, as per mail
>>>>> from Jeremy
>>>>> (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
>>>>>
>>>>> How do I get the fixed code into my galaxy instance?
>>>>>
>>>>> Thanks,
>>>>> -Raj
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> 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:
>>>>> http://lists.bx.psu.edu/
>>>>>
>>>>> 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:
>>> http://lists.bx.psu.edu/
>>>
>>> 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:
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To search Galaxy mailing lists use the unified search at:
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