can we get mysql bin log file access

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Shefali Vyas

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Jan 14, 2026, 4:30:15 PMJan 14

to genome...@soe.ucsc.edu

This is from Regeneron and we do use your data for our analysis purpose

Can we have mysql bin log file access

. UCSC sources: UCSC Genome Browser: Mirror Instructions;UCSC Genome Browser: 2Mirror Instructions

We are facing difficulties in rsync for the bigger sized data

Thanks

Shefali

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Hiram Clawson

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Jan 14, 2026, 5:04:42 PMJan 14

to Shefali Vyas, genome...@soe.ucsc.edu

Good Afternoon Shefali:

Can you clarify, what is it you are trying to access ?

--Hiram

On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific

Support wrote:
> Hi
>
> This is from Regeneron and we do use your data for our analysis purpose
>
> Can we have mysql bin log file access

> . UCSC sources: UCSC Genome Browser: Mirror Instructions<http://rohsdb.usc.edu/GBshape/admin/mirror.html>;UCSC Genome Browser: 2Mirror Instructions<https://hgdownload-test.gi.ucsc.edu/admin/mirror.html#step12>

Hiram Clawson

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Jan 14, 2026, 5:56:20 PMJan 14

to Shefali Vyas, genome...@soe.ucsc.edu

There are no .log files, you do not need .log files.

The database files you copy are complete by themselves. That
is all you need to copy the database.

--Hiram

On 1/14/26 2:50 PM, Shefali Vyas wrote:
> We are getting files in .frm , .idb, myd files from site with rsync
> rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/ /my/local/hg19/
>
>
> can I get .log (mysql bin log files)
>
> thanks
> shefali

>
> From: Hiram Clawson <hi...@soe.ucsc.edu>
> Sent: Wednesday, January 14, 2026 5:05 PM
> To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu
> Subject: [External] Re: [genome-mirror] can we get mysql bin log file access
>
> Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data
>

> EXTERNAL MESSAGE
> _________________________________________________________________

>
> Good Afternoon Shefali:
>
>
>
> Can you clarify, what is it you are trying to access ?
>
>
>
> --Hiram
>
>
>
> On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific
>
> Support wrote:
>
>> Hi
>
>>
>
>> This is from Regeneron and we do use your data for our analysis purpose
>
>>
>
>> Can we have mysql bin log file access
>

>> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>>;UCSC Genome Browser: 2Mirror Instructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$<https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>>

>
>>
>
>> We are facing difficulties in rsync for the bigger sized data
>
>>
>
>> Thanks
>
>> Shefali
>

Shefali Vyas

unread,

Jan 14, 2026, 6:00:24 PMJan 14

to Hiram Clawson, genome...@soe.ucsc.edu

We are getting files in .frm , .idb, myd files from site with rsync

rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/ /my/local/hg19/

can I get .log (mysql bin log files)

thanks

shefali

From: Hiram Clawson <hi...@soe.ucsc.edu>

Sent: Wednesday, January 14, 2026 5:05 PM
To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu

Subject: [External] Re: [genome-mirror] can we get mysql bin log file access

Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data

EXTERNAL MESSAGE
_________________________________________________________________

Good Afternoon Shefali:

Can you clarify, what is it you are trying to access ?

--Hiram

On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific

Support wrote:

> Hi

> This is from Regeneron and we do use your data for our analysis purpose

> Can we have mysql bin log file access

> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>;UCSC Genome Browser: 2Mirror Instructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>

> We are facing difficulties in rsync for the bigger sized data

> Thanks

> Shefali

********************************************************************

Shefali Vyas

unread,

Jan 14, 2026, 6:30:17 PMJan 14

to Hiram Clawson, genome...@soe.ucsc.edu

Actually that is too large to copy

If I can have log files I can apply CDC change data control and can get delta value to be applied

Thanks

Shefali

From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Wednesday, January 14, 2026 5:56 PM
To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu
Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access

EXTERNAL MESSAGE
_________________________________________________________________

>> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>>;UCSCGenome Browser: 2Mirror Instructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$<https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>>

Hiram Clawson

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Jan 14, 2026, 6:44:38 PMJan 14

to Shefali Vyas, genome...@soe.ucsc.edu

I'm confused, what is too large, the entire database directory
or individual files ? What is it that prevents you from copying
a large file ?

Here are the largest files in hg19 over 10 Gb:

-rwxr-xr-x 1 10216168630 Jul 7 2017 snp150OrthoPt5Pa2Rm8.MYD
-rwxr-xr-x 1 11040111764 Sep 9 2015 snp144OrthoPt4Pa2Rm3.MYD
-rwxr-xr-x 1 11376970108 Sep 3 2014 cacTest100way.MYD
-rwxr-xr-x 1 11447900732 Mar 24 2017 snp149OrthoPt4Pa2Rm3.MYD
-rwxr-xr-x 1 11574443868 Jul 17 2015 mafSnp100way.MYD
-rw-rw---- 1 12018946524 Sep 29 11:06 gnfAtlas2Distance.MYD
-rwxr-xr-x 1 13202232258 May 5 2017 snp150.MYD
-rwxr-xr-x 1 16739478940 May 8 2017 snp150OrthoPt4Pa2Rm3.MYD
-rwxr-xr-x 1 17429291156 Apr 15 2018 snp151Seq.MYD
-rwxr-xr-x 1 17979338064 May 23 2013 wgEncodeRegTfbsClusteredV3Slow.MYD
-rwxr-xr-x 1 17999062068 May 1 2013 wgEncodeRegTfbsClusteredV3b.MYD
-rwxr-xr-x 1 20414944532 Sep 6 2015 snp144.MYD
-rwxr-xr-x 1 21273639592 Oct 13 2016 snp147packtest.MYD
-rwxr-xr-x 1 21468641692 Mar 23 2017 snp149.MYD
-rwxr-xr-x 1 44607753960 Apr 18 2018 snp151OrthoPt5Pa2Rm8.MYD
-rwxr-xr-x 1 60805767208 Apr 15 2018 snp151.MYD
-rwxr-xr-x 1 114241937548 Mar 20 2019 encode3RegTfbsWithModsCluster.MYD

There are no .log files or incremental steps to these tables.
These tables are loaded once by one command and they are static
after that. Note the dates on those files, they are almost 10 years old.

>> To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>

>
>> Subject: [External] Re: [genome-mirror] can we get mysql bin log file access
>
>>
>
>> Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data
>
>>
>
>> EXTERNAL MESSAGE
>
>> _________________________________________________________________
>
>>
>
>> Good Afternoon Shefali:
>
>>
>
>>
>
>>
>
>> Can you clarify, what is it you are trying to access ?
>
>>
>
>>
>
>>
>
>> --Hiram
>
>>
>
>>
>
>>
>
>> On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific
>
>>
>
>> Support wrote:
>
>>
>
>>> Hi
>
>>
>
>>>
>
>>
>
>>> This is from Regeneron and we do use your data for our analysis purpose
>
>>
>
>>>
>
>>
>
>>> Can we have mysql bin log file access
>
>>
>

Shefali Vyas

unread,

Jan 14, 2026, 7:00:18 PMJan 14

to Hiram Clawson, genome...@soe.ucsc.edu

I am having this at my side

[root@tarritdb02p databases]# du -sh *

4.0K auto.cnf

4.0K backup

107G bosTau7

27G bosTau8

13G canFam1

35G canFam2

68G canFam3

1.6G cb1

4.0K checkdb.sh

9.4G chlSab2

28G criGri1

101G criGriChoV1

30G criGriChoV2

95G customTrash

7.1G danRer11

4.0K db.txt

16G dm6

22M eboVir3

11G felCat3

16G felCat4

9.1G felCat5

16G felCat8

7.1G galGal2

12G galGal3

6.7G galGal4

16G galGal5

577G galGal6

0 go

135G go150121

15G hbv1

3.1M hg18

657G hg19

742G hg38

28K hg38Patch11

18M hg38Patch3

2.5G hgcentral

197G hgFixed

699M hgTemp

5.2M ib_buffer_pool

1.9G ibdata1

512M ib_logfile0

512M ib_logfile1

76M ibtmp1

0 loxAfr1

0 loxAfr2

29G loxAfr3

25G macFas5

4.0K mkdb.sh

300G mm10

96G mm9

4.0K mm9_cp

36M mysql

4.0K mysql_upgrade_info

46G oryCun2

12G panTro1

36G panTro2

30G panTro3

19G panTro4

26G panTro5

1.1M performance_schema

5.7G proteins150225

0 proteome

114G regenCho1

24G regenRn0

76G regenRn1

37G rheMac2

44G rheMac3

30G rheMac8

26G rn5

132G rn6

26G rn7

43G sp150225

520M staAur1

2.9G staAur2

0 status

35G susScr11

23G susScr3

676K sys

4.0K tarritdb02p.regeneron.regn.com.pid

8.0K tarritdb02p-slow.log

0 tmp

0 uniprot

0 uniProt

179M visiGene

[root@tarritdb02p databases]# ~

From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Wednesday, January 14, 2026 6:45 PM
To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu
Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access

EXTERNAL MESSAGE
_________________________________________________________________

>>> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>>;UCSC<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC>GenomeBrowser: 2Mirror Instructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$<https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e>

Hiram Clawson

unread,

Jan 14, 2026, 7:23:11 PMJan 14

to Shefali Vyas, genome...@soe.ucsc.edu

Can you please clarify what is failing ?

What command do you use to copy files, and what error does
it issue ?

>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu>>
>

>> Sent: Wednesday, January 14, 2026 5:56 PM
>

>> To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>
>

>> Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
>
>>
>
>> There are no .log files, you do not need .log files. The database files you copy are complete by themselves. That is all you need to copy the database. --Hiram On 1/14/26 2: 50 PM, Shefali Vyas wrote: > We are getting files in .frm , .idb,
>
>>
>
>> EXTERNAL MESSAGE
>
>> _________________________________________________________________
>
>>
>
>> There are no .log files, you do not need .log files.
>
>>
>
>>
>
>>
>
>> The database files you copy are complete by themselves. That
>
>>
>
>> is all you need to copy the database.
>
>>
>
>>
>
>>
>
>> --Hiram
>
>>
>
>>
>
>>
>
>> On 1/14/26 2:50 PM, Shefali Vyas wrote:
>
>>
>
>>> We are getting files in .frm , .idb, myd files from site with rsync
>
>>
>
>>> rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/ /my/local/hg19/
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>> can I get .log (mysql bin log files)
>
>>
>
>>>
>
>>
>
>>> thanks
>
>>
>
>>> shefali
>
>>
>
>>>
>
>>
>
>>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>
>
>>
>
>>> Sent: Wednesday, January 14, 2026 5:05 PM
>
>>
>

>
>>
>
>>> Subject: [External] Re: [genome-mirror] can we get mysql bin log file access
>
>>
>
>>>
>
>>
>
>>> Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data
>
>>
>
>>>
>
>>
>
>>> EXTERNAL MESSAGE
>
>>
>
>>> _________________________________________________________________
>
>>
>
>>>
>
>>
>
>>> Good Afternoon Shefali:
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>> Can you clarify, what is it you are trying to access ?
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>> --Hiram
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>>
>
>>
>
>>> On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific
>
>>
>
>>>
>
>>
>
>>> Support wrote:
>
>>
>
>>>
>
>>
>
>>>> Hi
>
>>
>
>>>
>
>>
>
>>>>
>
>>
>
>>>
>
>>
>
>>>> This is from Regeneron and we do use your data for our analysis purpose
>
>>
>
>>>
>
>>
>
>>>>
>
>>
>
>>>
>
>>
>
>>>> Can we have mysql bin log file access
>
>>
>
>>>
>
>>
>

Shefali Vyas

unread,

Jan 15, 2026, 3:30:17 PMJan 15

to Hiram Clawson, genome...@soe.ucsc.edu

Thank you so much for replies

So when the database size is 4.5 TB now

After rsync done the database needs to be restart and that restart is taking more than hour

What is coming as a downtime

So If I would have delta data instead of full data I can make CDC and can reduce downtime

Or change in design to reduce downtime

That is my purpose , your help and replies are really appreciated

Thanks

Shefali

From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Wednesday, January 14, 2026 7:23 PM
To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu
Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access

Can you please clarify what is failing ? What command do you use to copy files, and what error does it issue ? On 1/14/26 3: 49 PM, Shefali Vyas wrote: > Hi > > I am having this at my side > > [root@ tarritdb02p databases]# du -sh

EXTERNAL MESSAGE
_________________________________________________________________

Hiram Clawson

unread,

Jan 15, 2026, 4:02:58 PMJan 15

to Shefali Vyas, genome...@soe.ucsc.edu

We use these ISAM table formats precisely so we do not have
to start and stop the database when we do updates. When
we develop a new track, we simply rsync in the new table
files into the running database. We run a 'flush tables'
command and the new data is available immediately. Or you
can run a 'flush tables newTableName' to make it recognize
just that one new table.

If you want to be perfectly safe, you can rsync in the new
table files into temporary named files, then after the three
files are present you can rename the temporary named files into the
actual new table name set of files, then run the
'flush tables newTableName' to get the running system to
recognize the new table data. That will be pretty much
instantaneous to turn on the new table, no downtime
at all for the running system.

Our currently running MySQL server has been up for
more than a year:

12:57:39 up 379 days, 21:58, 2 users, load average: 3.34, 2.95, 3.38

ps -ef | grep -i mysql

mysql 4307 1 61 2024 ? 232-16:50:35 /usr/sbin/mariadbd

There is no need to start and stop the system with
these ISAM table types.

>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu>>
>

>> Sent: Wednesday, January 14, 2026 6:45 PM
>

>> To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>
>
>> Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
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>>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>
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>>> Sent: Wednesday, January 14, 2026 5:56 PM
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>>> To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com<mailto:shefal...@regeneron.com%3cmailto:shefal...@regeneron.com>>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu%3cmailto:genome...@soe.ucsc.edu>>
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>>> Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
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>>> There are no .log files, you do not need .log files. The database files you copy are complete by themselves. That is all you need to copy the database. --Hiram On 1/14/26 2: 50 PM, Shefali Vyas wrote: > We are getting files in .frm , .idb,
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>>> EXTERNAL MESSAGE
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>>> _________________________________________________________________
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>>> There are no .log files, you do not need .log files.
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>>> The database files you copy are complete by themselves. That
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>>> is all you need to copy the database.
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>>> --Hiram
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>>> On 1/14/26 2:50 PM, Shefali Vyas wrote:
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>>>> We are getting files in .frm , .idb, myd files from site with rsync
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>>>> rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/ /my/local/hg19/
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>>>> can I get .log (mysql bin log files)
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>>>> thanks
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>>>> shefali
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>>>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>>
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>>>> Sent: Wednesday, January 14, 2026 5:05 PM
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>>>> Subject: [External] Re: [genome-mirror] can we get mysql bin log file access
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>>>> Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data
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>>>> Good Afternoon Shefali:
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>>>> --Hiram
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>>>> On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific
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>>>> Support wrote:
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>>>>> Hi
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>>>>> This is from Regeneron and we do use your data for our analysis purpose
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>>>>> Can we have mysql bin log file access
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Shefali Vyas

unread,

Jan 15, 2026, 4:30:20 PMJan 15

to Hiram Clawson, genome...@soe.ucsc.edu

Understood let me check with my team then why we perform the same

Thanks for the clarification

I was actually planning to take delta but seems not required

Thanks will test and let you know

And again thanks so much for your valued support

Shefali

From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Thursday, January 15, 2026 4:03 PM
To: Shefali Vyas <shefal...@regeneron.com>; genome...@soe.ucsc.edu
Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access

EXTERNAL MESSAGE
_________________________________________________________________

>>>>> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>>;UCSC<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC>Genome<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome>Browser:<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome%3eBrowser:>2MirrorInstructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$<https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3e><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3e%3e%3e>

Shefali Vyas

unread,

Jan 16, 2026, 10:30:16 AMJan 16

to Hiram Clawson, genome...@soe.ucsc.edu

Just came to know in database there are ibd files too

./mysql/engine_cost.ibd

./mysql/time_zone.ibd

./rn5/REGNratrn5.ibd

./rn5/trackDb_localTracks.ibd

./sys/sys_config.ibd

./hg38/crispr10KRanges.ibd

./hg38/grp_local.ibd

./hg38/crispr10KTargets.ibd

./hg38/trackDb_localTracks.ibd

./hg38/REGNBAC.ibd

./hg38/REGNCrispr.ibd

./hg38/REGNHumanRecomb.ibd

./hg38/REGNInsertion.ibd

./hg38/REGNTaqman.ibd

./macFas5/hgFindSpec.ibd

./macFas5/trackDb.ibd

./regenCho1/trackDb.ibd

[root@tarritdb02p databases]# find . -type f -name "*.ibd" |wc -l

4507

[root@tarritdb02p databases]#

So again now any help for getting DELTA changes from the site ?

Thanks

shefali

Regeneron - Internal

EXTERNAL MESSAGE
_________________________________________________________________

>>>>> . UCSC sources: UCSC Genome Browser: Mirror Instructions<https://urldefense.com/v3/__http://rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$>>;UCSC<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC>Genome<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome>Browser:<https://urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3chttps:/urldefense.com/v3/__http:/rohsdb.usc.edu/GBshape/admin/mirror.html__;!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nF-PiNIzQ$%3e%3e;UCSC%3eGenome%3eBrowser:>2MirrorInstructions<https://urldefense.com/v3/__https://hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$<https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$>><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3e><https://urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3chttps:/urldefense.com/v3/__https:/hgdownload-test.gi.ucsc.edu/admin/mirror.html*step12__;Iw!!ODpDvJZr5w!HFgD2PMkZjJpzU1cs1JB0fy93R1jrzHdVy_RHBbDyjKosRi_YuXbqxKuAhqOfv69Mm81VbkRgMvL1nFLgm1xng$%3e%3e%3e%3e%3e%3e%3e>

Hiram Clawson

unread,

Jan 16, 2026, 12:17:37 PMJan 16

to Shefali Vyas, genome...@soe.ucsc.edu

Good Morning Shefali:

Maybe you could help me understand what type of process you
are using there that prevents the rsync of the tables and
the 'flush tables' procedure I mentioned that we use to
update these tables in a running MySQL server.

There is no delta log file, it is not necessary with the
mechanism we use to maintain these databases. We simply
rsync copy the table files into the servers and use 'flush tables'
to enable their use. If we are updating an existing table,
we use the method of transferring the files into a temporary
name first, then simply 'rm oldTableFiles' 'mv tmpFiles updatedFiles'
and 'flush tables'

We only use INNODB tables for three very specific tables that are rapidly
changing. And these are tables you would not be transferring since they
are management tables in the hgcentral database specific to the installation.
We do not have INNODB tables for the vast majority of tables in
these assembly databases. If you are finding them locally in your
installation, these are probably tables you created there and they were
created as INNODB if the MySQL configuration settings had not been set
to make ISAM tables by default. You would not be copying INNODB tables
from us. Our three INNODB tables in hgcentral:

-rw-rw---- 1 9437184 Jan 16 08:51 /data/mysql/hgcentral/hubSpace.ibd
-rw-rw---- 1 14583595008 Jan 16 09:10 /data/mysql/hgcentral/userDb.ibd
-rw-rw---- 1 20443037696 Jan 16 09:10 /data/mysql/hgcentral/sessionDb.ibd

--Hiram

Mark Diekhans

unread,

Jan 16, 2026, 2:30:15 PMJan 16

to Shefali Vyas, Hiram Clawson, genome...@soe.ucsc.edu

Hi Shefali,

As Hiram said, there are no deltas for MyISAM. They do not
exist as the technology does not support transactions. These
tables are replaced as a whole by our internal rsync from the
development server.

We only use InnoDB for read/write tables that are not
downloadable, like user session data.

Find these InnoDB table files is alarming, as they conflict with
standard UCSC tables:
./macFas5/hgFindSpec.ibd
./macFas5/trackDb.ibd

It seems you may have do this

The first thing I would do determine what is causing the very
long startup time. There might be some information in mysql
logs. Could it be unrelated to the rsync?

My guess is that if it is the UCSC table rsync, it might be
mysql recovering tables mark as crashed. That is only a guess,
need to make sure.

Fundamentally, it is not safe to overwrite table files in a
running mysql server. Even if these are read-only, a partially
written file, or inconsistencies between the track.MYD, track.MYI,
and track.frm during the copy, could cause mysql to mark the table
as crashed.

The only safe way to replace the table files is to do it with
the knowledge of MySQL. This is straight-forward, but requires
some scripting.

1) rsync the new/modified table files to a temporary directory
on the same file system as the database files. Using the the
same file system allows for fast renames vs copies.

2) move the files into the correct directory with a modified
name than that indicates it is new
mv track.MYD mysql/hg38/track_new.MYD
mv track.MYI mysql/hg38/track_new.MYI
mv track.frm mysql/hg38/track_new.frm

3) in mysql do a
FLUSH TABLES;

4) rename the tables in one command:
RENAME TABLE track track_old, track_new track;
FLUSH TABLES;

The atomic rename using one command ensure the table
doesn't disappear.

5) delete the track_old.* files
the FLUSH TABLES ensured that mysql doesn't have the track_old table
open

> > From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu>>
>

> > Sent: Wednesday, January 14, 2026 7:23 PM
>

> > To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>
>
> > Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
>
> >
>

> >> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>
>
> >
>

> >> Sent: Wednesday, January 14, 2026 6:45 PM
>
> >
>

> >> To: Shefali Vyas <shefal...@regeneron.com<mailto:shefal...@regeneron.com<mailto:shefal...@regeneron.com%3cmailto:shefal...@regeneron.com>>>; genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu%3cmailto:genome...@soe.ucsc.edu>>
>
> >
>
> >> Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
>
> >
>
> >>
>
> >
>

> >>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>>
>
> >
>
> >>
>
> >
>

> >>> Sent: Wednesday, January 14, 2026 5:56 PM
>
> >
>
> >>
>
> >
>

> >>> Subject: Re: [External] Re: [genome-mirror] can we get mysql bin log file access
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>> There are no .log files, you do not need .log files. The database files you copy are complete by themselves. That is all you need to copy the database. --Hiram On 1/14/26 2: 50 PM, Shefali Vyas wrote: > We are getting files in .frm , .idb,
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>> EXTERNAL MESSAGE
>
> >
>
> >>
>
> >
>
> >>> _________________________________________________________________
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>> There are no .log files, you do not need .log files.
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>> The database files you copy are complete by themselves. That
>
> >
>
> >>
>
> >
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> >>>
>
> >
>
> >>
>
> >
>
> >>> is all you need to copy the database.
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
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> >>
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> >
>
> >>>
>
> >
>
> >>
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> >
>
> >>> --Hiram
>
> >
>
> >>
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> >
>
> >>>
>
> >
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> >>
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> >
>
> >>>
>
> >
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> >>
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> >
>
> >>>
>
> >
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> >>
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> >
>
> >>> On 1/14/26 2:50 PM, Shefali Vyas wrote:
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> We are getting files in .frm , .idb, myd files from site with rsync
>
> >
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> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/ /my/local/hg19/
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
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> >
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> >>
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> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
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> >>
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> >
>
> >>>
>
> >
>
> >>
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> >
>
> >>>> can I get .log (mysql bin log files)
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
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> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> thanks
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> shefali
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> From: Hiram Clawson <hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu<mailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu%3cmailto:hi...@soe.ucsc.edu>>>>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> Sent: Wednesday, January 14, 2026 5:05 PM
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>

>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> Subject: [External] Re: [genome-mirror] can we get mysql bin log file access
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> Good Afternoon Shefali: Can you clarify, what is it you are trying to access ? --Hiram On 1/14/26 1: 01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific Support wrote: > Hi > > This is from Regeneron and we do use your data
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
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> >
>
> >>>>
>
> >
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> >>
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> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> EXTERNAL MESSAGE
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> _________________________________________________________________
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> Good Afternoon Shefali:
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
>
> >>
>
> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>>
>
> >
>
> >>
>
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> >>>
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> >>>>
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> >>
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> >
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> >>>
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> >>
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> >
>
> >>>> Can you clarify, what is it you are trying to access ?
>
> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>
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> >>
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> >>>
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> >>>>
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> >>
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> >>>
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> >>
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> >>>>
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> >>
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> >>>
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> >>
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> >
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> >>>> --Hiram
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> >>
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> >
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> >>>
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> >>
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> >
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> >>>>
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> >>
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> >>>
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> >>>>
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> >>>
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> >>>>
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> >>>
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> >>
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> >
>
> >>>> On 1/14/26 1:01 PM, 'Shefali Vyas' via UCSC Genome Browser Mirror-Specific
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >>>>
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> >>
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> >>>
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> >>>> Support wrote:
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> >>>
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> >>
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> >
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> >>>>
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> >>
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> >>>
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> >>
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> >>>>> Hi
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> >>
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> >>>
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> >>
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> >
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> >>>>
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> >>>
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> >>>>>
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> >>>
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> >>>>
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> >>
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> >
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> >>>
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> >
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> >>
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> >
>
> >>>>> This is from Regeneron and we do use your data for our analysis purpose
>
> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>>
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> >>
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> >
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> >>>
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> >>
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
>
> >>>>> Can we have mysql bin log file access
>
> >
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> >>
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> >
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> >>>
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> >>
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> >
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> >>>>
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> >>
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> >>>
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> >>
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>

>
> >>>>>
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> >>
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> >>>
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> >>
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
>
> >>>>> We are facing difficulties in rsync for the bigger sized data
>
> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>> Thanks
>
> >
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> >>
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> >
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> >>>
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> >>
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> >
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
>
> >>>>> Shefali
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> >
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> >>
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> >
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> >>>
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> >
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> >>
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> >
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> >>>>
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> >
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> >>
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> >
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> >>>
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> >>
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> >
>
> >>>> ********************************************************************
>
> >
>
> >>
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> >
>
> >>>
>
> >
>
> >>
>
> >
>
> >>>> This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party.
>
> >
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> >>
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> >
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> >>>
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> >>
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> >>>> ********************************************************************
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> >
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> >>>>
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> >>
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> >>
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> >>
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> >
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> >
>
>

> --
>
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