faToTwoBit: not found / trackster

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faToTwoBit: not found / trackster

Jasper Jan Koehorst

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:

http://pastebin.com/9fZrkRDn

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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Re: faToTwoBit: not found / trackster

Jeremy Goecks-3
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.

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

On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <[hidden email]> 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:

http://pastebin.com/9fZrkRDn

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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Re: faToTwoBit: not found / trackster

Jeremy Goecks
In reply to this post by Jasper Jan Koehorst
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 <[hidden email]> 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:

http://pastebin.com/9fZrkRDn

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:
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Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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Re: faToTwoBit: not found / trackster

Jasper Koehorst
In reply to this post by Jasper Jan Koehorst
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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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:
>
> http://pastebin.com/9fZrkRDn
>
> 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"
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Re: faToTwoBit: not found / trackster

Jasper Jan Koehorst
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 <[hidden email]>
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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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:
>
> http://pastebin.com/9fZrkRDn
>
> 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:
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Re: faToTwoBit: not found / trackster

Jeremy Goecks-3
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 <[hidden email]> 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 <[hidden email]>
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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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:
>
> http://pastebin.com/9fZrkRDn
>
> 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/


___________________________________________________________
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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Re: faToTwoBit: not found / trackster

Jeremy Goecks-3
In reply to this post by Jasper Jan Koehorst
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 <[hidden email]> 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 <[hidden email]>
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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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:
>
> http://pastebin.com/9fZrkRDn
>
> 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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___________________________________________________________
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___________________________________________________________
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