Re: [galaxy-dev] faToTwoBit: not found / trackster
Yes and i even chmodded it to 777 for testing purposes. When I run it I get the option overview of the tool. I can't copy that right now (out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error.
Best, J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl<mailto:jasper.koehorst@wur.nl>> wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
{'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,049 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
, 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
: : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
'/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
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To give a better answer, when I enter the command this is what I get: :~$ faToTwoBit faToTwoBit - Convert DNA from fasta to 2bit format usage: faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit options: -noMask Ignore lower-case masking in fa file. -stripVersion Strip off version number after '.' for GenBank accessions. -ignoreDups Convert first sequence only if there are duplicate sequence names. Use 'twoBitDup' to find duplicate sequences. 2014/1/4 Jasper Koehorst <jasperkoehorst@gmail.com>
Yes and i even chmodded it to 777 for testing purposes. When I run it I get the option overview of the tool. I can't copy that right now (out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error.
Best, J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl <mailto:jasper.koehorst@wur.nl>> wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error
in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error
in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
{'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03
17:24:37,049 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
, 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets
ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
: : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
'/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1:
faToTwoBit: not found\n'}
}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error
in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error
in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET
/api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
___________________________________________________________ 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/
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Ok, then it's very likely a PATH issue. There's no magic needed here - faToTwoBit simply needs to be on your path. It seems you've tried debugging this already; one suggestion is to provide the full path to the executable and see if that works. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Jan 6, 2014, at 1:49 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl> wrote:
To give a better answer, when I enter the command this is what I get:
:~$ faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMask Ignore lower-case masking in fa file.
-stripVersion Strip off version number after '.' for GenBank accessions.
-ignoreDups Convert first sequence only if there are duplicate sequence
names. Use 'twoBitDup' to find duplicate sequences.
2014/1/4 Jasper Koehorst <jasperkoehorst@gmail.com> Yes and i even chmodded it to 777 for testing purposes. When I run it I get the option overview of the tool. I can't copy that right now (out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error.
Best, J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl<mailto:jasper.koehorst@wur.nl>> wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
{'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,049 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
, 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
: : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
'/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
___________________________________________________________ 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/
Ok, then it's very likely a PATH issue. There's no magic needed here - faToTwoBit simply needs to be on your path. It seems you've tried debugging this already; one suggestion is to provide the full path to the executable and see if that works. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Jan 6, 2014, at 1:49 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl> wrote:
To give a better answer, when I enter the command this is what I get:
:~$ faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMask Ignore lower-case masking in fa file.
-stripVersion Strip off version number after '.' for GenBank accessions.
-ignoreDups Convert first sequence only if there are duplicate sequence
names. Use 'twoBitDup' to find duplicate sequences.
2014/1/4 Jasper Koehorst <jasperkoehorst@gmail.com> Yes and i even chmodded it to 777 for testing purposes. When I run it I get the option overview of the tool. I can't copy that right now (out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error.
Best, J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl<mailto:jasper.koehorst@wur.nl>> wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
{'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,049 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
, 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
{{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
: : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
'/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show
rval = self._data( trans, dataset, **kwd )
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"
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participants (3)
-
Jasper Jan Koehorst -
Jasper Koehorst -
Jeremy Goecks