mafFrags errors with .hg.conf

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Katya Khalizeva

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Jun 30, 2021, 3:01:28 PMJun 30
to gen...@soe.ucsc.edu
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

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Jul 2, 2021, 3:33:32 PMJul 2
to Katya Khalizeva, UCSC Genome Browser Discussion List

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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Host a workshop: https://bit.ly/ucscTraining


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Katya Khalizeva

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Jul 14, 2021, 6:12:38 PMJul 14
to Jairo Navarro Gonzalez, UCSC Genome Browser Discussion List
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

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Jul 14, 2021, 7:43:54 PMJul 14
to Katya Khalizeva, UCSC Genome Browser Discussion List

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

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