mafFrags errors with .hg.conf

[Katya Khalizeva]

Hi,

I am trying to use the mafFrags tool but I keep getting errors. Here is an example of a command I am trying to run: mafFrags mm9 multiz30way -bed12 in.bed out.maf

I have set up the .hg.conf file in my home directory, which looks like this:

db.host=genome-mysql.cse.ucsc.edu

db.user=genomep

db.password=password

central.db=hgcentral

central.host=genome-mysql.cse.ucsc.edu

central.user=genomep

central.password=password

backupcentral.db=hgcentral

backupcentral.host=genome-mysql.cse.ucsc.edu

backupcentral.user=genomep

backupcentral.password=password

However, I have been getting error messages saying the following: 

cartTablesOk failed on hgcentral.userDb  pid=55469

hConnectCentral failed over to backupcentral pid=55469

cartTablesOk failed on hgcentral.userDb  pid=55469

Cannot access cart tables in central (nor backupcentral) database.  Please check central and backupcentral settings in the hg.conf file and the databases they specify.

I have not been able to find a solution for this online, and I was wondering if you could help me figure out what's wrong and how to get the mafFrags command to work. Thank you so much!

Best,

Katya

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and reporting your issues.

An engineer has discovered that the following line needs to be added to your hg.conf file:

forceTwoBit=on

If this still does not resolve the problem, please do not hesitate to contact us again.

I hope this is helpful. 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.

Jairo Navarro
UCSC Genome Browser

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[Katya Khalizeva]

Hello!

Thank you for your help! Adding that line to the .hg.conf file worked, however now I am getting these errors, and I was wondering what the issue might be:

TCP non-blocking connect() to hgdownload.soe.ucsc.edu timed-out in select() after 10000 milliseconds - Cancelling!
Couldn't open http://hgdownload.soe.ucsc.edu/gbdb/mm9/mm9.2bit

TCP non-blocking connect() to hgdownload.soe.ucsc.edu timed-out in select() after 10000 milliseconds - Cancelling!
Operation now in progress
Couldn't open http://hgdownload.soe.ucsc.edu/gbdb/mm9/multiz30way/anno/maf/chr1.maf

Thanks again!

Best,

Katya

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the Genome Browser and reporting your issues.

An engineer shares that you might be experiencing a networking issue. Are you able to
download these files when using your web browser? Could you send us the output of the
following command:

curl -I http://hgdownload.soe.ucsc.edu/gbdb/mm9/mm9.2bit

I look forward to your response. 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.

Jairo Navarro
UCSC Genome Browser

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining