I've had a problem with gdal_calc for a few days that I didn't have before.
Basically, I should recalculate a GEO file and I've always used (via Anaconda Prompt):
python %CONDA_PREFIX%\Scripts\gdal_calc.py -A myfile.geo --outfile mynewfile.geo --calc="-(A*5/7)" --format=ENVI --NoDataValue=-9999 --overwrite
I've never had any problems, but since a few days, trying to convert a GEO file I get:
could not open file "file.geo"
I tried to convert the initially converted files back without problems and:
pressing Enter, I get nothing
I get the same error
I would like to understand where the problem could be.
I state that I have not made any changes to the path of the GDAL and Anaconda files
I run this command:
COPY XXX FROM 'D:/XXX.csv' WITH (FORMAT CSV, HEADER TRUE, NULL 'NULL')
In Windows 7, it successfully imports CSV files of less than 1GB.
If the file is more then 1GB big, I get an “unknown error”.
[Code: 0, SQL State: XX000] ERROR: could not stat file "'D:/XXX.csv' Unknown error
How can I fix this issue?
You can work around this by piping the file through a program. For example I just used this to copy from a 24GB file on Windows 10 and PostgreSQL 11.
copy t(c,d) from program 'cmd /c "type x:\path\to\file.txt"' with (format text);
This copies the text file file.txt into the table t, columns c and d.
The trick here is to run cmd in a single command mode, with /c and telling it to type out the file in question.
https://github.com/MIT-LCP/mimic-code/issues/493
alistairewj commented Nov 3, 2018 • ►
edited
Okay, the could not stat file "CHARTEVENTS.csv": Unknown error is actually a bug in PostgreSQL 11. Under the hood it makes a call to fstat() to make sure the file is not a directory, and unfortunately fstat() is a 32-bit program which can't handle large files like chartevents. I tested the build on Windows with PostgreSQL 10.5 and I didn't get this error so I think it's fairly new.
The best workaround is to keep the files compressed (i.e. keep them as .csv.gz files) and use 7zip to load in the data directly from compressed files. In testing this seemed to still work. There is a pretty detailed tutorial on how to do this here: https://mimic.physionet.org/tutorials/install-mimic-locally-windows/
The brief version of above is that you keep the .csv.gz files, you add the 7zip binary to your windows environment path, and then you call the postgres_load_data_7zip.sql file to load in the data. You can use the postgres_checks.sql file after everything to make sure you loaded in all the data correctly.
edit: For your later error, where you are using this 7zip approach, I'm not sure why it's not loading. Try redownloading just the ADMISSIONS.csv.gz file and seeing if it still throws you that same error. Maybe there is a new version of 7zip which requires me to update the script or something!
For anyone else who googled this Postgres error message after attempting to work with a >1gb file in Postgres 11, I can confirm that #亚军吴's answer above is spot-on. It is indeed a size issue.
I tried a different approach, though, than #亚军吴's and #Loren's: I simply uninstalled Postgres 11 and installed the stable version of Postgres 10.7. (I'm on Windows 10, by the way, in case that matters.)
I re-ran the original code that had prompted the error and voila, a few minutes later I'd filled in a new table with data from a medium-ish-size csv file (~3gb). I initially tried to use CSVSplitter, per #Loren, which was working fine until I got close to running out of storage space on my machine. (Thanks, Battlefield 5.)
In my case, there isn't anything in PGSQL 11 that I was relying on that wasn't in version 10.7, so I think this could be a good solution for anyone else who runs into this problem. Thanks everyone above for contributing, especially to the OP for posting this in the first place. I cured a huge, huge headache!
This has been fixed in commit bed90759f in PostgreSQL v14.
The file limit for the error is actually 4 GB.
The fix was too invasive to be backported, so you can only upgrade to avoid the problem. Once the fix has had some field testing, you could lobby the pgsql-hackers mailing list to get it backported.
With pgAdmin and AWS, I used CSVSplitter to split into files less than 1GB. Lame, but worked. pgAdmin import appends to the existing table. (Changed escape character from ' to " in order to avoid error due to unquoted text in the source file. Typically I apply quotes in LibreOffice, but these files were too big to open.)
It seems this is not a database problem, but a problem of psql / pgadmin. The workaround is using an admin software from the previous psql versions:
Use the existing PostgreSQL 11 database
Install psql or pgadmin from the PostgreSQL 10 installation and use it to upload the file (with the command shown in the question)
Hope this helps anyone coming across the same problem.
Add two lines to your CSV file: One at the begining and one at the end:
COPY XXX FROM STDIN WITH (FORMAT CSV, HEADER TRUE, NULL 'NULL');
<here are the lines your file already contains>
\.
Don't forget another newline after the \. line. Then call
psql -h hostname -d dbname -U username -f 'D:/XXX.csv'
This is what worked for me:
\COPY member_data.lab_result FROM PROGRAM 'gzip -dcf lab_result.dat.gz' WITH (FORMAT 'csv', DELIMITER '|', QUOTE '`')
I don't know much about the command line but have been using it a lot lately. I was experiencing errors in a C application when trying to copy a file which didn't make sense; so, I tried using the the command line to make sure the code should work and get an error I don't understand.
copy "AH/Copy testing/media.enc" "AH/Copy testing/new_name.enc" returns the system cannot find the specified file. So, I tried type "AH/Copy testing/media.enc" and get the same error.
However, if change the directory to "AH/Copy testing", then type media.enc it works.
I tried the same statements on different files of the same and different extensions and they all work. For example, type "AH/Copy testing/fileName.enc" works.
Why would media.enc not be found unless the directory is set to its own first? If I copy media.enc to other locations, I get the same error unless the directory is first changed.
Thank you.
I have written a command file in mac which puts a particular file recognized by temp_todaysdate into s3 bucket and I am also printing size of the file(temp_todaysdate). When I am running this file manually in terminal, it is working fine i.e it is printing the size of file as well as putting the file to s3 bucket.
But when I am scheduling a cronjob to run this commnad file daily. I am getting a mail with the following error:
Size of file: 66520
./Bucket.command:line 10: aws2: command not found.
What can be done to resolve this error. Please help
I'm trying to combine two files using Windows command. However I keep getting the error:
The system cannot find the file specified.
The two files I'm trying to combine are .txt if that helps.
Edit: Another error popped up in addition to the original error, which said
Error occurred while processing filename