答复: [genome-mirror] Can't open /gbdb/hg19/hg19.2bit to read: Permission denied
程 维晟
Thank you for reply. When I give 'others' permission to read the file, it is still have the problem.
发送自 Windows 10 版邮件应用
发送时间: Saturday, March 3, 2018 3:25:39 AM
收件人: 程 维晟
抄送: genome...@soe.ucsc.edu
主题: Re: [genome-mirror] Can't open /gbdb/mm9/mm9.2bit to read: Permission denied
Hello Weisheng,
Thank you for using the UCSC Genome Browser and your inquiry.
The issue may be due to permissions given to the mm9.2bit file. Although you can open and read the contents of a folder on your server, the genome browser may not have permission to read a file within the folder. Please try editing the 2bit file so you give 'others' permission to read the file.
chmod o+r mm9.2bit
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 Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
--Dear sir:
I have some problems that need your help. When I zoom in to the base level, it show “ Can't open /gbdb/mm9/mm9.2bit to read: Permission denied”.
But in our server the attribute of folder is “drwxr-xr-x. 19 apache apache 4.0K Feb 13 04:39 mm9”. How can I fix it.
I look forward to your reply, so your early response will be greatly appreciated.
Sincerely yours,
Weisheng Cheng
Zhongshan School of Medicine
Sun Yat-sen University
Room 418 of Science and Technology building
Zip 510080
Tel: 86-18127924231
E-mail: cws...@hotmail.com
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Jairo Navarro Gonzalez
Hello Weisheng,
Thank you for your follow-up question.
You previously reported experiencing the error on the mm9.2bit file; however, you shared the permissions for hg19, hg38, and hg19.2bit. If you are still experiencing errors with the mm9.2bit file, please make sure that you updated the permissions for the mm9.2bit file.
From your previous message, it appears the directory /gbdb is a soft link to /home/public_resource.file/bigData/gbdb/. One of our engineers has shared that you need to check permissions of all directories in the path to /gbdb/mm9/mm9.2bit to verify access. All directories in the 'real' path (pwd -P) must be verified to be at least 755.
e.g., if bigData/ doesn't have public read and execute permissions, then you will get a permissions error on the 2bit file.
The following StackExchange post may be helpful:
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 Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
程 维晟
发件人: Jairo Navarro Gonzalez
发送时间: 2018年3月13日 23:41
收件人: 程
维晟
主题: Re: 答复:
答复: [genome-mirror] Can't open /gbdb/hg19/hg19.2bit to read: Permission denied
Hello Weisheng,
May I ask that you please forward your email to gen...@soe.ucsc.edu? This way our entire team will have an opportunity to view your question and other users may also benefit from our answers. Thanks for your understanding in this matter.
Jairo Navarro
UCSC Genomics Institute
On Mon, Mar 12, 2018 at 7:27 PM, 程 维晟 <cws...@hotmail.com> wrote:
Dear sir，
I have found the problem,In the browserSetup.sh, it says that
If your current disk space is not sufficient, you can
“mv /gbdb /bigData/gbdb && ln -s /bigData/gbdb /gbdb, mv /var/lib/mysql /bigData/mysql && ln -s /bigData/mysql /var/lib/mysql"
But I find that, if I do this “mv /var/lib/mysql /bigData/mysql && ln -s /bigData/mysql /var/lib/MySQL”,the MySQL cannot start,
And we mount a hard disk, the MySQL can start.
We still do “mv /gbdb /bigData/gbdb && ln -s /bigData/gbdb /gbdb”, and we can download the files,
but it still have the problem “Can't open /gbdb/hg19/hg19.2bit to read: Permission denied”.
And we mount a hard disk, the file can be read through web.
So we need mount the hard disk, But not use the symlink.
I hope this is helpful for others.
发送自 Windows 10 版邮件应用
发件人: Jairo Navarro Gonzalez
发送时间: 2018年3月7日 6:05
收件人: 程 维晟
抄送: gen...@soe.ucsc.edu
主题: Re: 答复: [genome-mirror] Can't open /gbdb/hg19/hg19.2bit to read: Permission denied
Hello Weisheng,
Thank you for your follow-up question.
You previously reported experiencing the error on the mm9.2bit file; however, you shared the permissions for hg19, hg38, and hg19.2bit. If you are still experiencing errors with the mm9.2bit file, please make sure that you updated the permissions for the mm9.2bit file.
From your previous message, it appears the directory
/gbdbis a soft link to/home/public_resource.file/bigData/gbdb/. One of our engineers has shared that you need to check permissions of all directories in the path to/gbdb/mm9/mm9.2bitto verify access. All directories in the 'real' path (pwd -P) must be verified to be at least 755.e.g., if bigData/ doesn't have public read and execute permissions, then you will get a permissions error on the 2bit file.
The following StackExchange post may be helpful:
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 Genomics InstituteWant to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
On Fri, Mar 2, 2018 at 7:25 PM, 程 维晟 <cws...@hotmail.com> wrote:
Thank you for reply. When I give 'others' permission to read the file, it is still have the problem.
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