I am trying to run the standalone ncbi-blast-2.2.28+ on my machine (Mac) but get this error message when running blastp with SwissProt database:
BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file (/Users/me/bin/db/swissprot.00).
Here what I did:
1) downloaded the "ncbi-blast-2.2.28+-universal-macosx.tar.gz" from ncbi server and decompressed it
2) move the bin content of the folder to my $PATH directory "/Users/me/bin"
3) In "/Users/me/bin" I created a "db" folder, plus the ".ncbirc" file containing the following path:
[BLAST]
BLASTDB=/Users/me/bin/db
4) I downloaded the SwissProt database and got the following files in "/Users/me/bin/db/:
swissprot.00.msk
swissprot.01.msk
swissprot.02.msk
swissprot.03.msk
swissprot.04.msk
swissprot.05.msk
swissprot.06.msk
swissprot.07.msk
swissprot.08.msk
swissprot.09.msk
swissprot.10.msk
swissprot.00.pal
swissprot.01.pal
swissprot.02.pal
swissprot.03.pal
swissprot.04.pal
swissprot.05.pal
swissprot.06.pal
swissprot.07.pal
swissprot.08.pal
swissprot.09.pal
swissprot.10.pal
swissprot.pal
Then when I run blastp from any working directory (where my query file is), using this command:
blastp -query input.fasta -db swissprot
I get the following error message:
BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file (/Users/me/bin/db/swissprot.00).
As I read on other threads, I also tried to mention in the command line the whole path where the db is located, and to remove the .pal extension from the file names. But still doesn't work.
Can someone sees what I did wrong ?!!!!
you are storing your database files in db folder so you have to give this command instead of the one you have used:
blastp -query input.fasta -db db/swissprot
and I believe you are looking for an output in the console itself as you haven't used the -out option.
Also this will work only if the bin directory in which db folder is present be declared as an environment variable.
Have you checked the paths in .pal file?
Swissprot database that you have downloaded contains only links to entries in nr database: "nr - Non-redundant GenBank CDS translations + PDB + SwissProt + PIR + PRF, excluding those in env_nr". So you should additionally download nr database to run the standalone blast on your machine with SwissProt database. It weighs about 20 (!) Gb, but without it your blast will not work. Here's a link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/
place all files from 00 to 10 folders into db and then check .pal file should contain 00 to 10 parts for example for nr databas its like
"nr.00" "nr.01" "nr.02" "nr.03" "nr.04" "nr.05" "nr.06" "nr.07" "nr.08" "nr.09" "nr.10"
Related
Load data infile has always been a pain in the ass to set up and there does not seem to be standard way to get it to work but I have always been able to get it to work ….eventually except now.
I am struggling with
Error Code: 29. File '/loadinfile/file.csv' not found (OS errno 13 - Permission denied)
The system is as follows:
MySQL version 8.0.29-0ubuntu0.22.04.2
Ubuntu 22.04
The load file directory is owned by mysql:mysql and same with the file and I have tried chmod 757 and even 777
In the config file I have tried the following variations:
secure_file_priv = "/loadinfile/"
secure_file_priv = '/loadinfile/'
secure_file_priv = ""
secure_file_priv = ''
The following is also set :
[mysqld]
local-infile = 1
[client]
loose-local-infile=1
Changing
LOAD DATA INFILE '/loadinfile/file.csv' INTO TABLE table
to
LOAD DATA LOCAL INFILE '/loadinfile/file.csv' INTO TABLE table
changes the error message to:
Error Code: 2. File '\loadinfile\file.csv' not found (OS errno 2 - No such file or directory)
Error Code: 2. File '\loadinfile\file.csv' not found (OS errno 2 - No such file or directory)
Above message indicates that your directory where the file is located is wrong! You must define the full path:
For example In Mac If your file resides on Desktop,It must be like this :
LOAD DATA LOCAL INFILE '/Users/computer_name/Desktop/filename.file_extension' INTO TABLE table
In windows
LOAD DATA LOCAL INFILE 'C:\Users\computer_name\Desktop\filename.file_extension' INTO TABLE table
I hope It solves your problem.
Error Code: 2. indicates invalid file path. Keep the LOCAL INFILE option and either specify the full path of the CSV file or make sure the CSV file path is correct. give it a try with Full path and see if it solves the problem or not.
From MySQL Docs
If LOCAL is specified, the file must be located on the client host.
The client program reads the file, locating it as follows:
If the file name is an absolute path name, the client program uses it
as given.
If the file name is a relative path name, the client program looks for
the file relative to its invocation directory
Edited
Make sure your mysqld.cnf or your main MySQL config file has the following variables
secure_file_priv = ""
local_infile=1
And your Global variable local_infile is OFF, turn it ON.
you can check that if you run this query
SHOW GLOBAL VARIABLES LIKE 'local_infile';
if it is OFF, turn it ON
And lastly, Make sure you restart your SQL service to reflect the changes. you can do that if you execute
service mysql restart
Hope that solves your problem
Im attempting to source a file 2019Dump.sql within another file solution2.sql.
Use a backup file 2019Dump.sql to load the pre 01 January 2020 contents of
relational tables LOCATED, SERVES and ORDERS into the database abc123.
I am running the solution2.sql through terminal using source solution2.sql.
when I run solution2.sql it is meant to source and run 2019Dump.sql.
I have tried 2 methods that (I have found and both error (42000)
source 2019Dump.sql;
mysql -u root -p abc123 < 2019Dump.sql;
I am trying to convert VMX to OVF format using OVFTool as below, however it gives error:
C:\Program Files\VMware\VMware OVF Tool>ovftool.exe
vi://vcenter.com:port/folder/myfolder/abc.vmx abc.ovf
Error: Failed to open file: https://vcenter.com:port/folder/myfolder/abc.vmx
Completed with errors
Please let me know if you have any solution.
I had a similar situation in vmware fusion trying to use a .vmx that was probably created on windows. I could boot the VM, but any attempt to export the machine with ovftool or use vmware-vdiskmanager bombed out with:
Error: Failed to open disk: source.vmdk
Completed with errors
the diskname was totally valid, path was valid, permissions were valid, and the only clue was running ovftool with:
ovftool --X:logToConsole --X:logLevel=verbose source.vmx dest.ova
Opening VMX source: source.vmx
verbose -[10C2513C0] Opening source
verbose -[10C2513C0] Failed to open disk: ./source.vmdk
verbose -[10C2513C0] Exception: Failed to open disk: source.vmdk. Reason: Disk encoding error
Error: Failed to open disk: source.vmdk
as others suggested, i took a peek in the .vmdk. therein i found 3 other clues:
encoding="windows-1252"
createType="monolithicSparse"
# Extent description
RW 16777216 SPARSE "source.vmdk"
so first i converted the monolithicSparse vmdk to "preallocated virtual disk split in 2GB files":
vmware-vdiskmanager -r source.vmdk -t3 foo.vmdk
then i could edit the "foo.vmdk" to change the encoding, which now looks like:
encoding="utf-8"
createType="twoGbMaxExtentFlat"
# Extent description
RW 8323072 FLAT "foo-f001.vmdk" 0
RW 8323072 FLAT "foo-f002.vmdk" 0
RW 131072 FLAT "foo-f003.vmdk" 0
and finally, after fixing up the source.vmx:
scsi0:0.fileName = "foo.vmdk"
profit:
ovftool source.vmx dest.ova
...
Opening VMX source: source.vmx
Opening OVA target: dest.ova
Writing OVA package: dest.ova
Transfer Completed
Completed successfully
I had a similar problem with OVFTool trying to export to OVF format.
Export failed: Failed to open file: C:\Virtual\test\test.vmx.
First, I opened .VMX file in editor (it's a text file) and made sure that settings like
scsi0:0.fileName = "test.vmdk"
nvram = "test.nvram"
extendedConfigFile = "test.vmxf"
mention proper file names.
Then I noticed this line:
.encoding = "windows-1251"
This is Cyrillic code page, so I modified it to use Western code page
.encoding = "windows-1252"
Then, running OVFTool gave a different error
Export failed: Failed to open disk: test.vmdk.
To fix it I had to open .VMDK file in HEX editor (because it's usually a big binary file), found there the string
encoding = "windows-1251"
(it's somewhere in the beginning of the file), and replaced "1251" with "1252".
And it did the trick!
In my case, was needed repair the disk 'abc.vmdk' before convert the 'abc.vmx' to 'abc.ovf'.
Use this for Linux:
$ /usr/bin/vmware-vdiskmanager -R /home/user/VMware/abc.vmdk
Look this link https://kb.vmware.com/s/article/2019259 for resolved issue in Windows and Linux
Try to run as described below.
C:\Program Files\VMware\VMware OVF Tool>ovftool C:\Win-Test\Win-Test.vmx(location of your vmx file) C:\Win-Test\win-test.ovf (destination)
Maybe ovftool is unable to recognize the path you are giving.
Try with following command:
ovftool --eula#=[path to eula] --X:logToConsole --targetType=OVA --compress=9 vi://[username]:[ESX address] [target address]
Once you provide the ESX address, it will list down the folders you have created in your ESX box. Then you can trigger the command above mentioned again with appending folder name.
If no folder hierarchy present in your box, then it will simply list down vm names.
Retry the same command appending [foldername]/[vmname no vmx file name required]
ovftool --eula#=[path to eula] --X:logToConsole --targetType=OVA --compress=9 vi://[username]:[ESX address]/[foldername if exist]/[vmname no vmx file name required] [target address]
I had this same exact issue. In my case I opened up the VMX file and dropped the IDE and sound controllers from the file and saved. I was then able to convert everything to an OVA using the tool with the standard syntax.
e.g. I dropped:
ide1:0.present = "TRUE"
ide1:0.deviceType = "cdrom-image"
and:
sound.present = "TRUE"
sound.fileName = "-1"
sound.autodetect = "TRUE"
This allowed me to convert the file like normal.
For me opening the .vmx and deleting the following line worked:
sata0:1.deviceType = "cdrom-image"
In my case, this works:
ide1:0.present = "TRUE"
ide1:0.deviceType = "cdrom-image"
I did change true to false and works fine, as cdrom-image not exist, this change permit the format conversion.
if your goal is to move a windows based vm to virtual box you only need to:
uninstall vmware tools from the guest vm
shut down the machine
copy the hd to a new folder
create a new empty vm in virtualbox
mount the hd (the .vmdk file) in that vm
Easy and rapid to do.
I am designing an application in Python and trying to write to a CSV file, but I am getting this error:
DatabaseError: 1 (HY000): Can't create/write to file '2015-04-06 20:48:33.418000'.csv (Errcode: 13 - Permission denied)
The Code:
def generate_report(self):
conn=mysql.connector.connect(user='root',password='',host='localhost',database='mydatabase')
exe2 = conn.cursor()
exe2.execute("""SELECT tbl_site.Site_name, State_Code, Country_Code,Street_Address, instrum_start_date, instrum_end_date, Comment INTO OUTFILE %s FIELDS TERMINATED BY '|' OPTIONALLY ENCLOSED BY '"' ESCAPED BY '\\\\' LINES TERMINATED BY '\\n'FROM tbl_site JOIN tbl_site_monit_invent ON site_id = tbl_Site_site_id """, (str(datetime.datetime.now()),))
I can run this code without any errors on a Mac, but I need it to work on Windows.
How can I resolve this error?
Simple really. A colon character is not a valid character in a filename on Windows. It's not allowed.
Reference: https://msdn.microsoft.com/en-us/library/windows/desktop/aa365247%28v=vs.85%29.aspx
The colon character is in the list of "reserved characters", along with several others. (NOTE: One use of the colon character is as a separator for an Alternate Data Stream on NTFS. Ref: http://blogs.technet.com/b/askcore/archive/2013/03/24/alternate-data-streams-in-ntfs.aspx
Followup
The question has been significantly edited since my previous answer was provided. Some notes:
I'm not very familiar with running MySQL on Windows OS. Most of my work with MySQL server is on Linux.
The SELECT ... INTO OUTFILE statement will cause the MySQL server to attempt to write a file on the server host.
The MySQL user (the user logged in to MySQL) must have the FILE privilege in order to use the SELECT ... INTO OUTFILE statement.
Also, the OS account that is running MySQL server must have OS permissions to write a file to the specified directory, and the file to be written must not already exist. Also, the filename must conform to the naming rules for filenames on OS filesystem.
Ref: https://dev.mysql.com/doc/refman/5.5/en/select-into.html
For debugging this type of issue, I strongly recommend you echo out the actual SQL text that is going to be sent to the MySQL server. And then take that SQL text and run it from a different client, like the mysql command line client.
For debugging a privileges issues, you can use a much simpler statement. Test writing a file to a directory that is known to exist, that is known the mysql server has permissions to write files to, and with a filename that does not exist and that conforms to the rules for the OS and filesystem.
For example, on a normal Linux box, we could test with something like this:
mysql> SELECT 'bar' AS foo INTO OUTFILE '/tmp/mysql_foo.csv'
Before we run that, we can easily verify that the /tmp directory exists, that it is writable by the OS account that is running the mysql server, and that the filename conforms to the rules for the filesystem, and that the filename doesn't exist, e.g.
$ su - mysql
$ ls -l /tmp/mysql_foo.csv
$ echo "foo" >/tmp/mysql_foo.csv
$ cat /tmp/mysql_foo.csv
$ rm /tmp/mysql_foo.csv
$ ls -l /tmp/mysql_foo.csv
Once we get over that hurdle, we can move on to testing writing a file to a different directory, a file with a more more complex filename. Once we get that plumbing working, we can work on getting actual data, into a usable csv format.
The original question seems to indicate that the MySQL server is running on Windows OS, and it seems to indicate that the filename attempting to be written contains semicolon characters. Windows does not allow semicolon as part a filename.
It was simply permission error.
When i try to source an sql file i get the error:
mysql> source C:/Users/tom/Documents/insert.sql
ERROR:
Failed to open file 'C:/Users/tom/Documents/insert.sql', error: 2
I have checked the file path, which looks fine to me. I have also tried \. C:/Users/etc
I am trying to source the sql file which holds insert statements for particular tables. All the statements in the file work when entered manually. What else could i be doing wrong?
Have tried using both backslash and forward slash when using this command
Probably a problem of access right on the file (the file is being accessed by the mysqld server process, not yourself). Try placing the file into the data folder of MySQL, then import it from this location. The location of data folder depends on your distribution and on your own configuration.
Alternatively, feed the SQL script directly to your mysql client's stdin:
mysql [all relevant options] your_database < C:\path\to\your\script.sql
I am using Ubuntu 14.04 version.
I too faced below error 2.
mysql> SOURCE home/loc/Downloads/AllTables.sql;
Failed to open file 'home/loc/Downloads/AllTables.sql', error: 2
Solution :
mysql> SOURCE /home/loc/Downloads/AllTables.sql;
Just added a '/' in front of home
Hope this helps some one.
Have you checked if the file exits? I have had this problem before.
This:
this:
and this works: