hgWiggle Cannot Find phastCons46way
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Kipper Fletez-Brant
Jun 30, 2014, 11:30:28 AM6/30/14
to gen...@soe.ucsc.edu
Hi,
I am trying to use hgWiggle to access the UCSC MySQL database to get
phastCons scores for regions of the human genome. Below is what I have
tried and the error message I get. Basically, even though I log into
the MySQL client and can see the table phastCons46way, hgWiggle cannot
access it. What am I doing wrong?
Thank you,
Kipper Fletez-Brant
*** Sample code and error messages ***
# attempt 1: just print all info for all bases
userApps/bin/hgWiggle -doStats -position=chr1:28125-28872 -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
# attempt 2: use a sample text file
userApps/bin/hgWiggle -doStats -bedFile=hgwiggleTest.txt -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
# attempt 3: just write whatever to screen
userApps/bin/hgWiggle -db=hg19 -position=chr1:28125-28872 -rawDataOut
-doStats phastCons46way
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
I am trying to use hgWiggle to access the UCSC MySQL database to get
phastCons scores for regions of the human genome. Below is what I have
tried and the error message I get. Basically, even though I log into
the MySQL client and can see the table phastCons46way, hgWiggle cannot
access it. What am I doing wrong?
Thank you,
Kipper Fletez-Brant
*** Sample code and error messages ***
# attempt 1: just print all info for all bases
userApps/bin/hgWiggle -doStats -position=chr1:28125-28872 -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
# attempt 2: use a sample text file
userApps/bin/hgWiggle -doStats -bedFile=hgwiggleTest.txt -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
# attempt 3: just write whatever to screen
userApps/bin/hgWiggle -db=hg19 -position=chr1:28125-28872 -rawDataOut
-doStats phastCons46way
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
Luvina Guruvadoo
Jun 30, 2014, 4:30:38 PM6/30/14
to Kipper Fletez-Brant, gen...@soe.ucsc.edu
Hello Kipper,
Thank you for your question. In order to run hgWiggle, you will need to download the .wib file into a local directory. Please refer to our instructions here: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
--
Kipper Fletez-Brant
Jul 1, 2014, 11:27:04 AM7/1/14
to Luvina Guruvadoo, gen...@soe.ucsc.edu
Hi Luvina,
I must be missing something simple. I have downloaded the necessary
.wib file (phastCons46way.wib in my case; link provided below), and
just to be sure I double checked that my .hg.conf matches that of your
website (I'm listing it below for completeness), and when I go to run
something simple I get the error listed below.
Please advise,
Kipper
# wib I downloaded
ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib
# my .hg.conf
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
central.db=hgcentral
# command and error, called from directory containing
phastCons46way.wib - why doesn't it use the local copy?
hgWiggle -db=hg19 -chr=chr22 phastCons46way
> to read
>
> --
>
>
I must be missing something simple. I have downloaded the necessary
.wib file (phastCons46way.wib in my case; link provided below), and
just to be sure I double checked that my .hg.conf matches that of your
website (I'm listing it below for completeness), and when I go to run
something simple I get the error listed below.
Please advise,
Kipper
# wib I downloaded
ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib
# my .hg.conf
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
central.db=hgcentral
# command and error, called from directory containing
phastCons46way.wib - why doesn't it use the local copy?
hgWiggle -db=hg19 -chr=chr22 phastCons46way
No such file or directory
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
mustOpenFd: Can't open /gbdb/hg19/multiz46way/phastCons46way.wib to read
On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo wrote:
> Hello Kipper,
>
> Thank you for your question. In order to run hgWiggle, you will need
> to download the .wib file into a local directory. Please refer to our
> instructions here:
> http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu
> <mailto:gen...@soe.ucsc.edu>. All messages sent to that address are
> Hello Kipper,
>
> Thank you for your question. In order to run hgWiggle, you will need
> to download the .wib file into a local directory. Please refer to our
> instructions here:
> http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu
> archived on a publicly-accessible forum. If your question includes
> sensitive data, you may send it instead to genom...@soe.ucsc.edu
> <mailto:genom...@soe.ucsc.edu>.
> sensitive data, you may send it instead to genom...@soe.ucsc.edu
>
> - - -
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
>
> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>
> Hi,
>
> I am trying to use hgWiggle to access the UCSC MySQL database to
> get phastCons scores for regions of the human genome. Below is
> what I have tried and the error message I get. Basically, even
> though I log into the MySQL client and can see the table
> phastCons46way, hgWiggle cannot access it. What am I doing wrong?
>
> Thank you,
> Kipper Fletez-Brant
>
> *** Sample code and error messages ***
>
> # attempt 1: just print all info for all bases
> userApps/bin/hgWiggle -doStats -position=chr1:28125-28872
> <tel:28125-28872> -db=hg19 phastCons46way -doAscii
> - - -
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
>
> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>
> Hi,
>
> I am trying to use hgWiggle to access the UCSC MySQL database to
> get phastCons scores for regions of the human genome. Below is
> what I have tried and the error message I get. Basically, even
> though I log into the MySQL client and can see the table
> phastCons46way, hgWiggle cannot access it. What am I doing wrong?
>
> Thank you,
> Kipper Fletez-Brant
>
> *** Sample code and error messages ***
>
> # attempt 1: just print all info for all bases
> userApps/bin/hgWiggle -doStats -position=chr1:28125-28872
> No such file or directory
> mustOpenFd: Can't open /gbdb/hg19/multiz46way/__phastCons46way.wib
> to read
>
> # attempt 2: use a sample text file
> userApps/bin/hgWiggle -doStats -bedFile=hgwiggleTest.txt -db=hg19
> phastCons46way -doAscii
> No such file or directory
> mustOpenFd: Can't open /gbdb/hg19/multiz46way/__phastCons46way.wib
>
> # attempt 2: use a sample text file
> userApps/bin/hgWiggle -doStats -bedFile=hgwiggleTest.txt -db=hg19
> phastCons46way -doAscii
> No such file or directory
> to read
>
> # attempt 3: just write whatever to screen
> userApps/bin/hgWiggle -db=hg19 -position=chr1:28125-28872
> <tel:28125-28872> -rawDataOut -doStats phastCons46way
>
> # attempt 3: just write whatever to screen
> userApps/bin/hgWiggle -db=hg19 -position=chr1:28125-28872
> No such file or directory
> mustOpenFd: Can't open /gbdb/hg19/multiz46way/__phastCons46way.wib
> to read
>
> --
>
>
Kipper Fletez-Brant
Jul 2, 2014, 11:28:24 AM7/2/14
to Luvina Guruvadoo, gen...@soe.ucsc.edu
I'm writing this so that anyone else having the same problem that I had
can get up to speed.
If you find yourself having gone through all of the steps in the set of
quoted emails and things still don't work, add the following 2 lines to
your .hg.conf:
gbdbLoc1=/path/to/relevant/WIB/file/
gbdbLoc2=http://hgdownload.cse.ucsc.edu/gbdb/
This seemed to fix it for me (I discovered this by grepping the kent src
tree files for mention of the /gbdb/ directory and discovered the file
ex.hg.conf, which explained in great detail many other possible settings)
can get up to speed.
If you find yourself having gone through all of the steps in the set of
quoted emails and things still don't work, add the following 2 lines to
your .hg.conf:
gbdbLoc1=/path/to/relevant/WIB/file/
gbdbLoc2=http://hgdownload.cse.ucsc.edu/gbdb/
This seemed to fix it for me (I discovered this by grepping the kent src
tree files for mention of the /gbdb/ directory and discovered the file
ex.hg.conf, which explained in great detail many other possible settings)
Brian Lee
Jul 2, 2014, 3:41:55 PM7/2/14
to Kipper Fletez-Brant, Luvina Guruvadoo, gen...@soe.ucsc.edu
Dear Kipper,
Thank you for using the UCSC Genome Browser and your helpful feedback, we have updated the wikipage to include recommendations to add the gbdbLoc1= path lines.
If you have any further questions or suggestions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
--
Kipper Fletez-Brant
Jul 2, 2014, 6:46:15 PM7/2/14
to Brian Lee, Luvina Guruvadoo, gen...@soe.ucsc.edu
Sorry, hit 'Send' too soon. The error message continues:
Couldn't connect to database hg19 on genome-mysql.cse.ucsc.edu as
genomep.
Unknown MySQL server host 'genome-mysql.cse.ucsc.edu' (2)
Can't get data socket for
http://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib
getaddrinfo() error on hostName=hgdownload.cse.ucsc.edu: No address
associated with hostname
On Wed 02 Jul 2014 06:32:20 PM EDT, Kipper Fletez-Brant wrote:
> Well, now I am especially confused. As of ~ 3:00 EDT, I started
> getting the error message below. I have changed no settings in any of
> my programs or config files. Is something happening with the browser?
>
> mustOpenFd: Can't open phastCons46way.wib to read
> getaddrinfo() error on hostName=hgdownload.cse.ucsc.edu: No address
> associated with hostname
>> gbdbLoc2=http://hgdownload.__cse.ucsc.edu/gbdb/
>> <http://genome-mysql.cse.ucsc.edu>
>>
>>
>> <http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database>.
>> <mailto:cafletezbrant@gmail.__com
>> to read
>>
>> --
>>
>>
>>
>> --
>>
>>
Couldn't connect to database hg19 on genome-mysql.cse.ucsc.edu as
genomep.
Unknown MySQL server host 'genome-mysql.cse.ucsc.edu' (2)
Can't get data socket for
http://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib
getaddrinfo() error on hostName=hgdownload.cse.ucsc.edu: No address
associated with hostname
On Wed 02 Jul 2014 06:32:20 PM EDT, Kipper Fletez-Brant wrote:
> Well, now I am especially confused. As of ~ 3:00 EDT, I started
> getting the error message below. I have changed no settings in any of
> my programs or config files. Is something happening with the browser?
>
> mustOpenFd: Can't open phastCons46way.wib to read
> getaddrinfo() error on hostName=hgdownload.cse.ucsc.edu: No address
> associated with hostname
>
> No such file or directory
> mustOpenFd: Can't open phastCons46way.wib to read
> No such file or directory
>
>
>
> On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
>> Dear Kipper,
>>
>> Thank you for using the UCSC Genome Browser and your helpful feedback,
>> we have updated the wikipage to include recommendations to add the
>> gbdbLoc1= path lines.
>>
>> If you have any further questions or suggestions, please reply to
>
>
> On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
>> Dear Kipper,
>>
>> Thank you for using the UCSC Genome Browser and your helpful feedback,
>> we have updated the wikipage to include recommendations to add the
>> gbdbLoc1= path lines.
>>
>> If you have any further questions or suggestions, please reply to
>> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent to
>> that address are archived on a publicly-accessible forum. If your
>> question includes sensitive data, you may send it instead to
>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
>>
>> that address are archived on a publicly-accessible forum. If your
>> question includes sensitive data, you may send it instead to
>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
>>
>> All the best,
>> Brian Lee
>>
>>
>>
>> On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant
>> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>>
>> I'm writing this so that anyone else having the same problem that
>> I had can get up to speed.
>>
>> If you find yourself having gone through all of the steps in the
>> set of quoted emails and things still don't work, add the
>> following 2 lines to your .hg.conf:
>>
>> gbdbLoc1=/path/to/relevant/__WIB/file/
>> Brian Lee
>>
>>
>>
>> On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant
>> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>>
>> I'm writing this so that anyone else having the same problem that
>> I had can get up to speed.
>>
>> If you find yourself having gone through all of the steps in the
>> set of quoted emails and things still don't work, add the
>> following 2 lines to your .hg.conf:
>>
>> gbdbLoc2=http://hgdownload.__cse.ucsc.edu/gbdb/
>> <http://hgdownload.cse.ucsc.edu/gbdb/>
>>
>> This seemed to fix it for me (I discovered this by grepping the
>> kent src tree files for mention of the /gbdb/ directory and
>> discovered the file ex.hg.conf, which explained in great detail
>> many other possible settings)
>>
>>
>> On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
>>
>> Hi Luvina,
>>
>> I must be missing something simple. I have downloaded the
>> necessary .wib file (phastCons46way.wib in my case; link
>> provided below), and just to be sure I double checked that my
>> .hg.conf matches that of your website (I'm listing it below
>> for completeness), and when I go to run something simple I get
>> the error listed below.
>>
>> Please advise,
>> Kipper
>>
>> # wib I downloaded
>>
>> ftp://hgdownload.cse.ucsc.edu/__gbdb/hg19/multiz46way/__phastCons46way.wib
>>
>> This seemed to fix it for me (I discovered this by grepping the
>> kent src tree files for mention of the /gbdb/ directory and
>> discovered the file ex.hg.conf, which explained in great detail
>> many other possible settings)
>>
>>
>> On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
>>
>> Hi Luvina,
>>
>> I must be missing something simple. I have downloaded the
>> necessary .wib file (phastCons46way.wib in my case; link
>> provided below), and just to be sure I double checked that my
>> .hg.conf matches that of your website (I'm listing it below
>> for completeness), and when I go to run something simple I get
>> the error listed below.
>>
>> Please advise,
>> Kipper
>>
>> # wib I downloaded
>>
>>
>>
>> <ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib>
>>
>> # my .hg.conf
>> db.host=genome-mysql.cse.ucsc.__edu
>>
>> <ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib>
>>
>> # my .hg.conf
>> <http://genome-mysql.cse.ucsc.edu>
>> db.user=genomep
>> db.password=password
>> central.db=hgcentral
>>
>> # command and error, called from directory containing
>> phastCons46way.wib - why doesn't it use the local copy?
>> hgWiggle -db=hg19 -chr=chr22 phastCons46way
>> No such file or directory
>> mustOpenFd: Can't open
>> /gbdb/hg19/multiz46way/__phastCons46way.wib to read
>> db.password=password
>> central.db=hgcentral
>>
>> # command and error, called from directory containing
>> phastCons46way.wib - why doesn't it use the local copy?
>> hgWiggle -db=hg19 -chr=chr22 phastCons46way
>> No such file or directory
>> mustOpenFd: Can't open
>>
>>
>>
>>
>> On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo wrote:
>>
>> Hello Kipper,
>>
>> Thank you for your question. In order to run hgWiggle, you
>> will need
>> to download the .wib file into a local directory. Please
>> refer to our
>> instructions here:
>>
>> http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database
>>
>>
>>
>> On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo wrote:
>>
>> Hello Kipper,
>>
>> Thank you for your question. In order to run hgWiggle, you
>> will need
>> to download the .wib file into a local directory. Please
>> refer to our
>> instructions here:
>>
>>
>>
>> <http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database>.
>>
>>
>> If you have any further questions, please reply to
>> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>.
>>
>> If you have any further questions, please reply to
>> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>> All messages sent to that address are
>> archived on a publicly-accessible forum. If your question
>> includes
>> sensitive data, you may send it instead to
>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
>> <mailto:genom...@soe.ucsc.__edu
>> archived on a publicly-accessible forum. If your question
>> includes
>> sensitive data, you may send it instead to
>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
>> <mailto:genom...@soe.ucsc.edu>>.
>>
>> - - -
>> Luvina Guruvadoo
>> UCSC Genome Bioinformatics Group
>>
>>
>>
>> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
>> <caflet...@gmail.com <mailto:caflet...@gmail.com>
>>
>> - - -
>> Luvina Guruvadoo
>> UCSC Genome Bioinformatics Group
>>
>>
>>
>> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
>> <mailto:cafletezbrant@gmail.__com
>> <mailto:caflet...@gmail.com>>> wrote:
>>
>> Hi,
>>
>> I am trying to use hgWiggle to access the UCSC MySQL
>> database to
>> get phastCons scores for regions of the human genome.
>> Below is
>> what I have tried and the error message I get.
>> Basically, even
>> though I log into the MySQL client and can see the table
>> phastCons46way, hgWiggle cannot access it. What am I
>> doing wrong?
>>
>> Thank you,
>> Kipper Fletez-Brant
>>
>> *** Sample code and error messages ***
>>
>> # attempt 1: just print all info for all bases
>> userApps/bin/hgWiggle -doStats
>> -position=chr1:28125-28872 <tel:28125-28872>
>> <tel:28125-28872 <tel:28125-28872>> -db=hg19
>>
>> Hi,
>>
>> I am trying to use hgWiggle to access the UCSC MySQL
>> database to
>> get phastCons scores for regions of the human genome.
>> Below is
>> what I have tried and the error message I get.
>> Basically, even
>> though I log into the MySQL client and can see the table
>> phastCons46way, hgWiggle cannot access it. What am I
>> doing wrong?
>>
>> Thank you,
>> Kipper Fletez-Brant
>>
>> *** Sample code and error messages ***
>>
>> # attempt 1: just print all info for all bases
>> userApps/bin/hgWiggle -doStats
>> -position=chr1:28125-28872 <tel:28125-28872>
>> phastCons46way -doAscii
>> No such file or directory
>> mustOpenFd: Can't open
>> /gbdb/hg19/multiz46way/____phastCons46way.wib
>> No such file or directory
>> mustOpenFd: Can't open
>> to read
>>
>> # attempt 2: use a sample text file
>> userApps/bin/hgWiggle -doStats
>> -bedFile=hgwiggleTest.txt -db=hg19
>> phastCons46way -doAscii
>> No such file or directory
>> mustOpenFd: Can't open
>> /gbdb/hg19/multiz46way/____phastCons46way.wib
>>
>> # attempt 2: use a sample text file
>> userApps/bin/hgWiggle -doStats
>> -bedFile=hgwiggleTest.txt -db=hg19
>> phastCons46way -doAscii
>> No such file or directory
>> mustOpenFd: Can't open
>> to read
>>
>> # attempt 3: just write whatever to screen
>> userApps/bin/hgWiggle -db=hg19
>> -position=chr1:28125-28872 <tel:28125-28872>
>> <tel:28125-28872 <tel:28125-28872>> -rawDataOut
>>
>> # attempt 3: just write whatever to screen
>> userApps/bin/hgWiggle -db=hg19
>> -position=chr1:28125-28872 <tel:28125-28872>
>> -doStats phastCons46way
>> No such file or directory
>> mustOpenFd: Can't open
>> /gbdb/hg19/multiz46way/____phastCons46way.wib
>> No such file or directory
>> mustOpenFd: Can't open
>> to read
>>
>> --
>>
>>
>>
>> --
>>
>>
Brian Lee
Jul 2, 2014, 8:10:49 PM7/2/14
to Kipper Fletez-Brant, Luvina Guruvadoo, gen...@soe.ucsc.edu
Dear Kipper,
Thank you for your message. You may need to place your wib file in a directory to match where hgWiggle will look for it, such as hg19/multiz46way from the working directory you define with your gbdbLoc1 line.
I added some example steps in the new "Using hgWiggle options" section: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database#Using_hgWiggle_options
If you add gbdbLoc1=/home/usrName/work/ to your .hg.conf file, in that /home/usrName/work/ directory you will want to make a hg19/multiz46way/ directory, and move your .wib file there.
If you have any further questions or suggestions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
On Wed, Jul 2, 2014 at 3:32 PM, Kipper Fletez-Brant <caflet...@gmail.com> wrote:
Well, now I am especially confused. As of ~ 3:00 EDT, I started getting the error message below. I have changed no settings in any of my programs or config files. Is something happening with the browser?
mustOpenFd: Can't open phastCons46way.wib to read
getaddrinfo() error on hostName=hgdownload.cse.ucsc.edu: No address associated with hostname
No such file or directory
mustOpenFd: Can't open phastCons46way.wib to read
On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
Dear Kipper,
Thank you for using the UCSC Genome Browser and your helpful feedback,
we have updated the wikipage to include recommendations to add the
gbdbLoc1= path lines.
If you have any further questions or suggestions, please reply to
gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent to
that address are archived on a publicly-accessible forum. If your
question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
All the best,
Brian Lee
On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant<caflet...@gmail.com <mailto:cafletezbrant@gmail.com>> wrote:
I'm writing this so that anyone else having the same problem that
I had can get up to speed.
If you find yourself having gone through all of the steps in the
set of quoted emails and things still don't work, add the
following 2 lines to your .hg.conf:
gbdbLoc1=/path/to/relevant/__WIB/file/
gbdbLoc2=http://hgdownload.__cse.ucsc.edu/gbdb/
<http://hgdownload.cse.ucsc.edu/gbdb/>
This seemed to fix it for me (I discovered this by grepping the
kent src tree files for mention of the /gbdb/ directory and
discovered the file ex.hg.conf, which explained in great detail
many other possible settings)
On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
Hi Luvina,
I must be missing something simple. I have downloaded the
necessary .wib file (phastCons46way.wib in my case; link
provided below), and just to be sure I double checked that my
.hg.conf matches that of your website (I'm listing it below
for completeness), and when I go to run something simple I get
the error listed below.
Please advise,
Kipper
# wib I downloaded
db.host=genome-mysql.cse.ucsc.__edu
<http://genome-mysql.cse.ucsc.edu>
db.user=genomep
db.password=password
central.db=hgcentral
# command and error, called from directory containing
phastCons46way.wib - why doesn't it use the local copy?
hgWiggle -db=hg19 -chr=chr22 phastCons46way
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/__phastCons46way.wib to read
On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo wrote:
Hello Kipper,
Thank you for your question. In order to run hgWiggle, you
will need
to download the .wib file into a local directory. Please
refer to our
instructions here:
<mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>.
All messages sent to that address are
archived on a publicly-accessible forum. If your question
includes
sensitive data, you may send it instead to
genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
<mailto:genom...@soe.ucsc.__edu
<mailto:genom...@soe.ucsc.edu>>.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
<caflet...@gmail.com <mailto:cafletezbrant@gmail.com>
<mailto:cafletezbrant@gmail.__com
<mailto:cafletezbrant@gmail.com>>> wrote:
Hi,
I am trying to use hgWiggle to access the UCSC MySQL
database to
get phastCons scores for regions of the human genome.
Below is
what I have tried and the error message I get.
Basically, even
though I log into the MySQL client and can see the table
phastCons46way, hgWiggle cannot access it. What am I
doing wrong?
Thank you,
Kipper Fletez-Brant
*** Sample code and error messages ***
# attempt 1: just print all info for all bases
userApps/bin/hgWiggle -doStats
-position=chr1:28125-28872 <tel:28125-28872>
<tel:28125-28872 <tel:28125-28872>> -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/____phastCons46way.wib
to read
# attempt 2: use a sample text file
userApps/bin/hgWiggle -doStats
-bedFile=hgwiggleTest.txt -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/____phastCons46way.wib
to read
# attempt 3: just write whatever to screen
userApps/bin/hgWiggle -db=hg19
-position=chr1:28125-28872 <tel:28125-28872>
<tel:28125-28872 <tel:28125-28872>> -rawDataOut
-doStats phastCons46way
No such file or directory
mustOpenFd: Can't open
Kipper Fletez-Brant
Jul 3, 2014, 11:43:07 AM7/3/14
to Brian Lee, gen...@soe.ucsc.edu, Luvina Guruvadoo
After following your advice, it worked for maybe 300 queries before I started getting the same at if error messages. As I haven't moved the WIB file, I am unclear why I am getting these 'file not found' errors.
On Jul 2, 2014 9:16 PM, "Kipper Fletez-Brant" <caflet...@gmail.com> wrote:
I am attempting this now and will report back later. However, I do not expect this to be the solution, as I successfully queried some 15k genomic regions before I started having problems (which was ~3:00 EDT)
On Wed 02 Jul 2014 08:10:27 PM EDT, Brian Lee wrote:
Dear Kipper,
Thank you for your message. You may need to place your wib file in a
directory to match where hgWiggle will look for it, such as
hg19/multiz46way from the working directory you define with your
gbdbLoc1 line.
I added some example steps in the new "Using hgWiggle options"
section:
http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database#Using_hgWiggle_options
If you add gbdbLoc1=/home/usrName/work/ to your .hg.conf file, in that
/home/usrName/work/ directory you will want to make a
hg19/multiz46way/ directory, and move your .wib file there.
If you have any further questions or suggestions, please reply to
gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent to
that address are archived on a publicly-accessible forum. If your
question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
All the best,
Brian Lee
On Wed, Jul 2, 2014 at 3:32 PM, Kipper Fletez-Brant
<caflet...@gmail.com <mailto:cafletezbrant@gmail.com>> wrote:
Well, now I am especially confused. As of ~ 3:00 EDT, I started
getting the error message below. I have changed no settings in
any of my programs or config files. Is something happening with
the browser?
mustOpenFd: Can't open phastCons46way.wib to read
getaddrinfo() error on hostName=hgdownload.cse.ucsc.__edu
<http://hgdownload.cse.ucsc.edu>: No address associated with hostname
No such file or directory
mustOpenFd: Can't open phastCons46way.wib to read
On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
Dear Kipper,
Thank you for using the UCSC Genome Browser and your helpful
feedback,
we have updated the wikipage to include recommendations to add the
gbdbLoc1= path lines.
If you have any further questions or suggestions, please reply to
gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
<mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>. All
messages sent to
that address are archived on a publicly-accessible forum. If your
question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
<mailto:genom...@soe.ucsc.__edu
<mailto:genom...@soe.ucsc.edu>>.
All the best,
Brian Lee
On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant
<caflet...@gmail.com <mailto:cafletezbrant@gmail.com>
<mailto:cafletezbrant@gmail.__com
<mailto:cafletezbrant@gmail.com>>> wrote:
I'm writing this so that anyone else having the same
problem that
I had can get up to speed.
If you find yourself having gone through all of the steps
in the
set of quoted emails and things still don't work, add the
following 2 lines to your .hg.conf:
gbdbLoc1=/path/to/relevant/____WIB/file/
gbdbLoc2=http://hgdownload.__c__se.ucsc.edu/gbdb/
<http://cse.ucsc.edu/gbdb/>
<http://hgdownload.cse.ucsc.__edu/gbdb/
<http://hgdownload.cse.ucsc.edu/gbdb/>>
This seemed to fix it for me (I discovered this by
grepping the
kent src tree files for mention of the /gbdb/ directory and
discovered the file ex.hg.conf, which explained in great
detail
many other possible settings)
On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
Hi Luvina,
I must be missing something simple. I have downloaded the
necessary .wib file (phastCons46way.wib in my case; link
provided below), and just to be sure I double checked
that my
.hg.conf matches that of your website (I'm listing it
below
for completeness), and when I go to run something
simple I get
the error listed below.
Please advise,
Kipper
# wib I downloaded
ftp://hgdownload.cse.ucsc.edu/____gbdb/hg19/multiz46way/____phastCons46way.wib
<ftp://hgdownload.cse.ucsc.edu/__gbdb/hg19/multiz46way/__phastCons46way.wib>
<ftp://hgdownload.cse.ucsc.__edu/gbdb/hg19/multiz46way/__phastCons46way.wib
db.host=genome-mysql.cse.ucsc.____edu
<http://genome-mysql.cse.ucsc.__edu
<http://genome-mysql.cse.ucsc.edu>>
db.user=genomep
db.password=password
central.db=hgcentral
# command and error, called from directory containing
phastCons46way.wib - why doesn't it use the local copy?
hgWiggle -db=hg19 -chr=chr22 phastCons46way
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/____phastCons46way.wib to read
On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo
wrote:
Hello Kipper,
Thank you for your question. In order to run
hgWiggle, you
will need
to download the .wib file into a local directory.
Please
refer to our
instructions here:
http://genomewiki.ucsc.edu/____index.php/Using_hgWiggle_____without_a_database
<http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database>
<http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database
<http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database>>.
If you have any further questions, please reply to
gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
<mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
<mailto:gen...@soe.ucsc.edu
<mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu
<mailto:gen...@soe.ucsc.edu>>>.
All messages sent to that address are
archived on a publicly-accessible forum. If your
question
includes
sensitive data, you may send it instead to
genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
<mailto:genom...@soe.ucsc.__edu
<mailto:genom...@soe.ucsc.edu>>
<mailto:genom...@soe.ucsc.
<mailto:genom...@soe.ucsc.>____edu
<mailto:genom...@soe.ucsc.__edu
<mailto:genom...@soe.ucsc.edu>>>.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
<caflet...@gmail.com
<mailto:cafletezbrant@gmail.com>
<mailto:cafletezbrant@gmail.__com
<mailto:cafletezbrant@gmail.com>>
<mailto:cafletezbrant@gmail.
<mailto:cafletezbrant@gmail.>____com
/gbdb/hg19/multiz46way/______phastCons46way.wib
to read
# attempt 2: use a sample text file
userApps/bin/hgWiggle -doStats
-bedFile=hgwiggleTest.txt -db=hg19
phastCons46way -doAscii
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/______phastCons46way.wib
to read
# attempt 3: just write whatever to screen
userApps/bin/hgWiggle -db=hg19
-position=chr1:28125-28872 <tel:28125-28872>
<tel:28125-28872 <tel:28125-28872>>
<tel:28125-28872 <tel:28125-28872>
<tel:28125-28872 <tel:28125-28872>>> -rawDataOut
-doStats phastCons46way
No such file or directory
mustOpenFd: Can't open
/gbdb/hg19/multiz46way/______phastCons46way.wib
to read
--
--
Kipper Fletez-Brant
Jul 3, 2014, 11:43:07 AM7/3/14
to Brian Lee, Luvina Guruvadoo, gen...@soe.ucsc.edu
I am attempting this now and will report back later. However, I do not
expect this to be the solution, as I successfully queried some 15k
genomic regions before I started having problems (which was ~3:00 EDT)
expect this to be the solution, as I successfully queried some 15k
genomic regions before I started having problems (which was ~3:00 EDT)
On Wed 02 Jul 2014 08:10:27 PM EDT, Brian Lee wrote:
> Dear Kipper,
>
> Dear Kipper,
>
> Thank you for your message. You may need to place your wib file in a
> directory to match where hgWiggle will look for it, such as
> hg19/multiz46way from the working directory you define with your
> gbdbLoc1 line.
>
> I added some example steps in the new "Using hgWiggle options"
> section:
> http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database#Using_hgWiggle_options
>
> If you add gbdbLoc1=/home/usrName/work/ to your .hg.conf file, in that
> /home/usrName/work/ directory you will want to make a
> hg19/multiz46way/ directory, and move your .wib file there.
>
> If you have any further questions or suggestions, please reply to
> directory to match where hgWiggle will look for it, such as
> hg19/multiz46way from the working directory you define with your
> gbdbLoc1 line.
>
> I added some example steps in the new "Using hgWiggle options"
> section:
> http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database#Using_hgWiggle_options
>
> If you add gbdbLoc1=/home/usrName/work/ to your .hg.conf file, in that
> /home/usrName/work/ directory you will want to make a
> hg19/multiz46way/ directory, and move your .wib file there.
>
> If you have any further questions or suggestions, please reply to
> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent to
> that address are archived on a publicly-accessible forum. If your
> question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
> All the best,
> Brian Lee
>
>
>
> that address are archived on a publicly-accessible forum. If your
> question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
> All the best,
> Brian Lee
>
>
>
> On Wed, Jul 2, 2014 at 3:32 PM, Kipper Fletez-Brant
> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>
> Well, now I am especially confused. As of ~ 3:00 EDT, I started
> getting the error message below. I have changed no settings in
> any of my programs or config files. Is something happening with
> the browser?
>
> mustOpenFd: Can't open phastCons46way.wib to read
> getaddrinfo() error on hostName=hgdownload.cse.ucsc.__edu
> <caflet...@gmail.com <mailto:caflet...@gmail.com>> wrote:
>
> Well, now I am especially confused. As of ~ 3:00 EDT, I started
> getting the error message below. I have changed no settings in
> any of my programs or config files. Is something happening with
> the browser?
>
> mustOpenFd: Can't open phastCons46way.wib to read
> <http://hgdownload.cse.ucsc.edu>: No address associated with hostname
>
>
> No such file or directory
> mustOpenFd: Can't open phastCons46way.wib to read
>
>
>
>
> On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
>
> Dear Kipper,
>
> Thank you for using the UCSC Genome Browser and your helpful
> feedback,
> we have updated the wikipage to include recommendations to add the
> gbdbLoc1= path lines.
>
> If you have any further questions or suggestions, please reply to
> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>
> No such file or directory
> mustOpenFd: Can't open phastCons46way.wib to read
>
>
>
>
> On Wed 02 Jul 2014 03:40:57 PM EDT, Brian Lee wrote:
>
> Dear Kipper,
>
> Thank you for using the UCSC Genome Browser and your helpful
> feedback,
> we have updated the wikipage to include recommendations to add the
> gbdbLoc1= path lines.
>
> If you have any further questions or suggestions, please reply to
> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>. All
> messages sent to
> that address are archived on a publicly-accessible forum. If your
> question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
> <mailto:genom...@soe.ucsc.__edu
> <mailto:genom...@soe.ucsc.edu>>.
>
> messages sent to
> that address are archived on a publicly-accessible forum. If your
> question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
> <mailto:genom...@soe.ucsc.__edu
> <mailto:genom...@soe.ucsc.edu>>.
>
> All the best,
> Brian Lee
>
>
>
> On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant
> Brian Lee
>
>
>
> On Wed, Jul 2, 2014 at 6:26 AM, Kipper Fletez-Brant
> <mailto:caflet...@gmail.com>>> wrote:
>
> I'm writing this so that anyone else having the same
> problem that
> I had can get up to speed.
>
> If you find yourself having gone through all of the steps
> in the
> set of quoted emails and things still don't work, add the
> following 2 lines to your .hg.conf:
>
>
> I'm writing this so that anyone else having the same
> problem that
> I had can get up to speed.
>
> If you find yourself having gone through all of the steps
> in the
> set of quoted emails and things still don't work, add the
> following 2 lines to your .hg.conf:
>
> gbdbLoc1=/path/to/relevant/____WIB/file/
> gbdbLoc2=http://hgdownload.__c__se.ucsc.edu/gbdb/
> <http://cse.ucsc.edu/gbdb/>
>
> <http://hgdownload.cse.ucsc.__edu/gbdb/
> gbdbLoc2=http://hgdownload.__c__se.ucsc.edu/gbdb/
> <http://cse.ucsc.edu/gbdb/>
>
> <http://hgdownload.cse.ucsc.__edu/gbdb/
> <http://hgdownload.cse.ucsc.edu/gbdb/>>
>
> This seemed to fix it for me (I discovered this by
> grepping the
> kent src tree files for mention of the /gbdb/ directory and
> discovered the file ex.hg.conf, which explained in great
> detail
> many other possible settings)
>
>
> On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
>
> Hi Luvina,
>
> I must be missing something simple. I have downloaded the
> necessary .wib file (phastCons46way.wib in my case; link
> provided below), and just to be sure I double checked
> that my
> .hg.conf matches that of your website (I'm listing it
> below
> for completeness), and when I go to run something
> simple I get
> the error listed below.
>
> Please advise,
> Kipper
>
> # wib I downloaded
>
> This seemed to fix it for me (I discovered this by
> grepping the
> kent src tree files for mention of the /gbdb/ directory and
> discovered the file ex.hg.conf, which explained in great
> detail
> many other possible settings)
>
>
> On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:
>
> Hi Luvina,
>
> I must be missing something simple. I have downloaded the
> necessary .wib file (phastCons46way.wib in my case; link
> provided below), and just to be sure I double checked
> that my
> .hg.conf matches that of your website (I'm listing it
> below
> for completeness), and when I go to run something
> simple I get
> the error listed below.
>
> Please advise,
> Kipper
>
> # wib I downloaded
> ftp://hgdownload.cse.ucsc.edu/____gbdb/hg19/multiz46way/____phastCons46way.wib
> <ftp://hgdownload.cse.ucsc.edu/__gbdb/hg19/multiz46way/__phastCons46way.wib>
>
>
> <ftp://hgdownload.cse.ucsc.__edu/gbdb/hg19/multiz46way/__phastCons46way.wib
> db.host=genome-mysql.cse.ucsc.____edu
> <ftp://hgdownload.cse.ucsc.edu/__gbdb/hg19/multiz46way/__phastCons46way.wib>
>
>
> <ftp://hgdownload.cse.ucsc.__edu/gbdb/hg19/multiz46way/__phastCons46way.wib
> <http://genome-mysql.cse.ucsc.__edu
> <http://genome-mysql.cse.ucsc.edu>>
>
> db.user=genomep
> db.password=password
> central.db=hgcentral
>
> # command and error, called from directory containing
> phastCons46way.wib - why doesn't it use the local copy?
> hgWiggle -db=hg19 -chr=chr22 phastCons46way
> No such file or directory
> mustOpenFd: Can't open
> /gbdb/hg19/multiz46way/____phastCons46way.wib to read
>
> db.user=genomep
> db.password=password
> central.db=hgcentral
>
> # command and error, called from directory containing
> phastCons46way.wib - why doesn't it use the local copy?
> hgWiggle -db=hg19 -chr=chr22 phastCons46way
> No such file or directory
> mustOpenFd: Can't open
>
>
>
>
>
> On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo
> wrote:
>
> Hello Kipper,
>
> Thank you for your question. In order to run
> hgWiggle, you
> will need
> to download the .wib file into a local directory.
> Please
> refer to our
> instructions here:
> http://genomewiki.ucsc.edu/____index.php/Using_hgWiggle_____without_a_database
>
>
>
>
> On Mon 30 Jun 2014 04:30:35 PM EDT, Luvina Guruvadoo
> wrote:
>
> Hello Kipper,
>
> Thank you for your question. In order to run
> hgWiggle, you
> will need
> to download the .wib file into a local directory.
> Please
> refer to our
> instructions here:
> <http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database>
>
> <http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database
> <http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database>>.
>
>
> If you have any further questions, please reply to
> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
> <mailto:gen...@soe.ucsc.edu
> <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu
> <mailto:gen...@soe.ucsc.edu>>>.
>
> All messages sent to that address are
> archived on a publicly-accessible forum. If your
> question
> includes
> sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
> <mailto:genom...@soe.ucsc.__edu
> <mailto:genom...@soe.ucsc.edu>>
> <http://genomewiki.ucsc.edu/__index.php/Using_hgWiggle___without_a_database
> <http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database>>.
>
>
> If you have any further questions, please reply to
> gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
> <mailto:gen...@soe.ucsc.edu
> <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu
> <mailto:gen...@soe.ucsc.edu>>>.
>
> All messages sent to that address are
> archived on a publicly-accessible forum. If your
> question
> includes
> sensitive data, you may send it instead to
> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>
> <mailto:genom...@soe.ucsc.__edu
> <mailto:genom...@soe.ucsc.edu>>
> <mailto:genom...@soe.ucsc.__edu
> <mailto:genom...@soe.ucsc.edu>>>.
>
> - - -
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
>
> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
> <caflet...@gmail.com
> <mailto:genom...@soe.ucsc.edu>>>.
>
> - - -
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
>
> On Sat, Jun 28, 2014 at 2:43 PM, Kipper Fletez-Brant
> <caflet...@gmail.com
> <mailto:cafletezbrant@gmail.
> <mailto:cafletezbrant@gmail.>____com
>
> <mailto:cafletezbrant@gmail.__com
> <mailto:cafletezbrant@gmail.>____com
>
> <mailto:cafletezbrant@gmail.__com
>
> to read
>
> # attempt 2: use a sample text file
> userApps/bin/hgWiggle -doStats
> -bedFile=hgwiggleTest.txt -db=hg19
> phastCons46way -doAscii
> No such file or directory
> mustOpenFd: Can't open
> /gbdb/hg19/multiz46way/______phastCons46way.wib
> to read
>
> # attempt 2: use a sample text file
> userApps/bin/hgWiggle -doStats
> -bedFile=hgwiggleTest.txt -db=hg19
> phastCons46way -doAscii
> No such file or directory
> mustOpenFd: Can't open
>
> to read
>
> # attempt 3: just write whatever to screen
> userApps/bin/hgWiggle -db=hg19
> -position=chr1:28125-28872 <tel:28125-28872>
> <tel:28125-28872 <tel:28125-28872>>
> <tel:28125-28872 <tel:28125-28872>
> to read
>
> # attempt 3: just write whatever to screen
> userApps/bin/hgWiggle -db=hg19
> -position=chr1:28125-28872 <tel:28125-28872>
> <tel:28125-28872 <tel:28125-28872>>
> <tel:28125-28872 <tel:28125-28872>>> -rawDataOut
>
> -doStats phastCons46way
> No such file or directory
> mustOpenFd: Can't open
>
> -doStats phastCons46way
> No such file or directory
> mustOpenFd: Can't open
Matthew Speir
Jul 18, 2014, 5:37:32 PM7/18/14
to Kipper Fletez-Brant, Brian Lee, gen...@soe.ucsc.edu, Luvina Guruvadoo
Hi Kipper,
Thank you for your question about using hgWiggle. We have been unable to reproduce the error on our end. Are you still experiencing issues using hgWiggle with a local wib file?
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about using hgWiggle. We have been unable to reproduce the error on our end. Are you still experiencing issues using hgWiggle with a local wib file?
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
<caflet...@gmail.com <mailto:caflet...@gmail.com>
<mailto:cafletezbrant@gmail.__com
<mailto:caflet...@gmail.com>
<mailto:cafletezbrant@gmail.__com
<mailto:caflet...@gmail.com>>
<mailto:cafletezbrant@gmail.
<mailto:cafletezbrant@gmail.>____com
<mailto:cafletezbrant@gmail.__com
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