read_bits64 error when loading large genomes/data into trackster
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-t...). How do I get the fixed code into my galaxy instance? Thanks, -Raj
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 <raj76@uga.edu> 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-t...). 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/
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 <raj76@uga.edu <mailto:raj76@uga.edu>> 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-t...). 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/
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 <raj76@uga.edu <mailto:raj76@uga.edu>> 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-t...).
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/
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/3a154b52090316dee61f4299... Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam <raj76@uga.edu> 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 <raj76@uga.edu <mailto:raj76@uga.edu>> 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-t...).
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/
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/3a154b52090316dee61f4299...
Best, J.
-- Jeremy Goecks Assistant Professor of Computational Biology George Washington University
On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam <raj76@uga.edu <mailto:raj76@uga.edu>> 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 <raj76@uga.edu <mailto:raj76@uga.edu> <mailto:raj76@uga.edu>> 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-t...).
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/
participants (2)
-
Jeremy Goecks -
Raj Ayyampalayam