I've made a fresh install of nextflow in a new computer, and I was trying to test the nf-core/rnaseq pipeline, but I am receiving the following error when executing:
Error executing process > 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)'
Command error:
.command.sh: line 3: /media/Data/nextflow-rnaseq/rnaseq/bin/check_samplesheet.py: Permission denied
I've checked the permissions for the file, and has all the executing permissions:-rwxrwxr-x. I've also tried to execute it using both my working environment and singularity, and keep finding the same error.
I've also tested my own pipeline, with another project root folder and its own bin folder with custom scripts in there, and I'm having the same error.
Does anyone know if I'm missing something I should have done to make the scripts in bin accessible to nextflow?
Nextflow version: 22.04.4.5706
As Steve pointed out in a comment, the issue was related to how the filesystem was mounted (noexec), and fixing that solves the problem
when i tried to load local data files into hive table,it report error while moving files.And i found the link,which give comments to fix this issue.I follow this step ,but it still can't work.
http://answers.mapr.com/questions/3565/getting-started-with-hive-load-the-data-from-sample-table txt-into-the-table-fails
After mkdir /user/hive/tmp,and set hive.exec.scratchdir= /user/hive/tmp,it still report RuntimeException Cannot make directory:file/user/hive/tmp/hive_2013* How can I fix this issue?Who are familiar with hive can help me?Thanks!
hive version is 0.10.0
hadoop version is 1.1.2
I suspect a permission issue here, because you are using MapR distribution.
Make sure that the user trying to create the directory has permissions to create the directory on CLDB.
Easy way to debug here is to do
$hadoop fs -chmod -R 777 /user/hive
and then try to load the data, to confirm if it's permission issue.
I just started using Apache, but when I try to run myPHPadmin, I get this error message:
1 - Can't create/write to file '/var/folders/w1/5yx2p9mj7w9bm67gdwhqxwsr0000gn/T/#sql1ba_3_0.MYI' (Errcode: 13)
Another post in the Stack Overflow suggested changing the permissions on the XAMPP file, my.cnf, with this command:
sudo chmod 600 my.cnf
I tried running the code in Mac Terminal, but the result was "No such file or directory."
Does anyone know what I should try next?
This is a permission problem on your datadir (where MySQL wants to write files). Normally, at MySQL installation, correct permissions are set for the user who runs mysqld.
Are you sure that MySQL was installed correctly as part of XAMPP installation?
Hi i am trying to install phpbb-reputation system i followed the xml file for installation but while executing install_reputation.php i am getting this error ERROR: Could not open the file ./styles/afterburnerafterburner_config.html for reading.There are many errors in the same fashin. where i gues it is not going inside afterburner/template folder where .html file exists. where should i check this?
More error samples:
Refreshing the proFormell template
ERROR: Could not open the file ./styles/proFormellcaptcha_recaptcha.html for reading.
Sounds like it's a permissions issue; if hosting on a LAMP server, just run chmod 755 * -R in the website root directory. Alternatively you could also change file permissions using an FTP client
I'm following the instructions found here.
When I try to run $ heroku pg:psql or $ heroku pg:psql HEROKU POSTGRESQL_BROWN I recieve the following error message:
! The local psql command could not be located ! For help
installing psql, see local-postgresql
I can't find anything useful on the link it gives me (it just links to the instructions I was already using, but further down the page) nor can I find this error anywhere else.
If I've missed anything you need to know to answer this, just let me know. I'm rather new to all this and teaching myself as I go.
I had same error even after installing Postgres locally.
But after seeing this
I saw that "pqsl" was not in the PATH so I then did
PATH=%PATH%;C:\Program Files\PostgreSQL\9.2\bin
which worked for me
I have since solved this myself. When I ran heroku pg:info it says the version number is 9.1.8, I was locally running 9.2
installing 9.1.8 and ensuring Path pointed to the appropriate folder solved the problem.
After you change the path, make sure to restart the terminal!
Set the PATH. To find out the PATH of your psql script (on mac) open the sql shell script from your finder in Applications/Postgres installation. This will give you a hint as to where it is installed. That opened a window which told me it is located here: /Library/PostgreSQL/8.4/scripts/runpsql.sh
Then, I set the PATH variable from the terminal window by typing:
$ PATH="/Library/PostgreSQL/8.4/bin:$PATH"
(depends on the location of your PostgreSQL installation, find your bin path first, another exp: /usr/local/Cellar/postgresql#9.6/9.6.8/bin)
OR.....
You can also connect to the shell by opening the shell directly from your postgres installation folder. Then enter the credentials. If you don't know the credentials, here is how to find them out:
$ heroku pg:info
=== HEROKU_POSTGRESQL_RED_URL (DATABASE_URL)
$ heroku pg:credentials HEROKU_POSTGRESQL_RED_URL
Top answer wouldn't work for me oddly, my system would not add the Path via cmd with administrator access (Not sure why).
So check this > Windows key > environment variables > system variables
And add the last line (your version may differ in the path)
Make sure you've installed the toolbelt as psql is installed by default.
However you also need to ensure you've installed a local copy of PostgreSQL; if you don't the toolbelt will be unable to find the native psql client.
Assuming you have installed a local copy of PostgreSQL, make sure you can execute psql from the command line directly (i.e make sure you PATH is set correctly ). If the command does not execute, check your PATH, if it does execute see if you can connect via the PSQL connection string provided in the Heroku control panel. If you can connect reinstall the toolbelt, if you are unable to connect provision another dev database and try again.
If there are still issues, I would suggest contacting Heroku support for assistance after verifying no API issues are listed on the status page located here.
I got rid if this annoying message on Windows by adding a path element without the spaces, i.e.
C:\Progra~1\PostgreSQL\9.4\data
instead of
“C:\Program Files\PostgreSQL\9.4\data”
I followed the instructions here: http://www.computerhope.com/issues/ch000549.htm, which worked for me if you prefer to go the point-and-click configuration of the PATH variable.
This type of error usually appears in the Windows environment, because if you do not update the PATH after installing Postgresql, heroku pg:psql command does not work.
So you need to update your PATH environment variable to add the bin directory of your Postgres installation. The directory will look like this:
C:\Program Files\PostgreSQL\<VERSION>\bin.
For more information, go to the Heroku in Local setup website:
heroku-postgresql: Local setup
I had the same problem and discovered that Heroku doesn't seem to provision the latest version of PostgreSQL by default. Where the Heroku Getting Started instructions said
heroku addons:create heroku-postgresql:hobby-dev
That provisioned a v10 database for some reason (which you can check by clicking on Heroku Postgres in the Add-ons tab of your dashboard). I deleted that database and provisioned a new database using the --version flag:
heroku addons:create heroku-postgresql:hobby-dev --version 11
As of now, at least, you can find the latest version of Postgres supported by Heroku at this link: https://devcenter.heroku.com/articles/heroku-postgresql#version-support-and-legacy-infrastructure
I'm writing this in early 2019, but according to the PostgreSQL website the next version (12) is "tentatively scheduled" for third quarter of 2019 so if you're reading this in late 2019 potentially the same problem will come up for v12 instead
On Mac you can use the following:
export PATH="/Library/PostgreSQL/12/bin/:$PATH"
The only solution that I found on Windows:
go to advanced system settings
go to environment variables
select Path variable and click Edit
add a new line and enter your bin directory path (C:\Program Files\PostgreSQL<version>\bin) and click ok
restart your terminal
enter your psql command (heroku pg:psql)