ERROR 1114 (HY000) at line 33471: The table 'snps' is full
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Josie
Oct 15, 2014, 12:08:20 PM10/15/14
to stacks...@googlegroups.com
Hello Julian and STACKS friends,
I've run into a problem I've not seen before regarding mysql databasing with stacks:
after running denovomap the other day, I got the following errors:
ERROR 1114 (HY000) at line 1: The table 'markers' is full
ERROR 1114 (HY000) at line 1: The table 'snps' is full
after doing some digging around, it looked like the mysql ibdata1 file in /var/lib was causing mysql problems (and also filling up ALL the space in my root!!), so I have been painstakingly cleaning it up using mysqldump by moving the necessary files into my home directory (where there is more space) etc etc
However, I have been trying to restore the STACKS mysql files
restore:# mysql -u root -p[root_password] [database_name] < dumpfilename.sql
However, I am still getting the same error from mysql "ERROR 1114 (HY000) at line 33471: The table 'snps' is full"
Sorry if this is more of a mysql problem in general, but I thought a discussion here may help in case anyone else runs into the same issues.
Thank you!!
Josie
p.s. please let me know if you need any other log files, info etc
I've run into a problem I've not seen before regarding mysql databasing with stacks:
after running denovomap the other day, I got the following errors:
ERROR 1114 (HY000) at line 1: The table 'markers' is full
ERROR 1114 (HY000) at line 1: The table 'snps' is full
after doing some digging around, it looked like the mysql ibdata1 file in /var/lib was causing mysql problems (and also filling up ALL the space in my root!!), so I have been painstakingly cleaning it up using mysqldump by moving the necessary files into my home directory (where there is more space) etc etc
However, I have been trying to restore the STACKS mysql files
restore:# mysql -u root -p[root_password] [database_name] < dumpfilename.sql
However, I am still getting the same error from mysql "ERROR 1114 (HY000) at line 33471: The table 'snps' is full"
Sorry if this is more of a mysql problem in general, but I thought a discussion here may help in case anyone else runs into the same issues.
Thank you!!
Josie
p.s. please let me know if you need any other log files, info etc
Josie
Nov 13, 2014, 9:29:09 AM11/13/14
to stacks...@googlegroups.com
Hi everyone,
I thought I would post the solution to my own problem, in case anyone runs into this too.
The problem was that mysql makes a storage file called ibdata1 that can grow in size if you are making lots of stacks (or other mysql) databases. This caused the tables in stacks to become full, even after databases were removed.
You can move this file and also follow various instructions online for preventing it getting very large in size.
If anyone has this problem, please post and I will give more details
Bests,
Josie
I thought I would post the solution to my own problem, in case anyone runs into this too.
The problem was that mysql makes a storage file called ibdata1 that can grow in size if you are making lots of stacks (or other mysql) databases. This caused the tables in stacks to become full, even after databases were removed.
You can move this file and also follow various instructions online for preventing it getting very large in size.
If anyone has this problem, please post and I will give more details
Bests,
Josie
ES
Oct 23, 2015, 11:46:03 AM10/23/15
to Stacks
Hi everyone,
I have the same problem, Josie could you provide us more details? thanks!
Josie
Oct 26, 2015, 7:02:53 AM10/26/15
to Stacks
Hi ES,
I followed Method 2 on this online guide: http://blog-en.openalfa.com/how-to-reduce-the-size-of-the-ibdata1-file-in-mysql
You can then restore your stacks databases back into mysql without the issue of ibdata getting too large. This stopped the stacks errors for me.
Hope this helps!
Josie
p.s. I started disabling the mysql component (-S option) when running denovomap and refmap to keep the number of mysql databases to a minimum.
I followed Method 2 on this online guide: http://blog-en.openalfa.com/how-to-reduce-the-size-of-the-ibdata1-file-in-mysql
You can then restore your stacks databases back into mysql without the issue of ibdata getting too large. This stopped the stacks errors for me.
Hope this helps!
Josie
p.s. I started disabling the mysql component (-S option) when running denovomap and refmap to keep the number of mysql databases to a minimum.
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