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
Related
I wrote a Singularity container that works just fine on my computer. However, when a colleague of mine tries to run it, he gets the error output
FATAL: container creation failed: failed to resolve session directory /usr/local/var/singularity/mnt/session: lstat /usr/local/var: no such file or directory
In the past, he could run containers I build. In fact, he used being able to run a container with the same recipe. The change was that the version of Singularity on the machine I use to build it was upgraded.
I entered the error in a search engine, and I only found a single hit, https://forum.image.sc/t/improving-cluster-supercomputer-performance-tesla-v100-volta-16-32gb-gpu/37459/8, in which this is not resolved.
Does anybody know a way to fix this? Or what the source of the problem is? Or a workaround, preferably one that does not require me to downgrade Singularity? (The machine on which I build it is shared between several users, that's why I don't want to do that.)
Okay, this was somewhat trivial to solve, we just had the colleague create the required folder,
mkdir -p /usr/local/var/singularity/mnt/{container,final,overlay,session}
I'm getting the following exception while trying to start the hive in Ubuntu 14.04 LTS,Caused by: java.sql.SQLException: Failed to create database 'metastore_db', see the next exception for details. Hadoop installation is correct and it's working fine. Please tell me anyone what's problem?
It is because you're not in the same folder where you have created your metadata. I was facing the same problem because I was in my main user folder. When I changed the folder from main user to hduser my hive stated working.
See the mistake
I tried to find the xml file but it was not their so I searched and found where it was.
Similar to #dk14, In my case, I was in a folder on which I had no permission to write as user, moved directory and worked fine.
The reason for above error is, the user through which you are login doesn't have permission to write in that particular directory. I mean the directory in which you are running the schematool command.
For example my setup of Apache Hive was in /opt/apache-hive-3.1.2-bin I ran the command :-
sudo chown -R hadoopusr /opt/apache-hive-3.1.2-bin/
it is happening because you are on the other folder than your hive is installed.
so first of all change directory to the folder where your hive is installed and you and after that try to run hive once again.
and the hive should work properly.
Best of luck.
After spending some(lot) of time I got that issue is with creating that directory metastore_db inside DERBY_HOME/bin path was already there and I didn't had admin access for this you either:
delete that folder by using admin rights.
open hive-site.xml inside HIVE_HOME/conf path open in notepad and check connection string there change the database name to something else, it worked for me.
Trying to set up Jenkins on one of my servers for the first time and think I might be missing something.
Jenkins 1.545
Phing 2.6.1
Jenkins builds give me the following output.
Building in workspace /var/www/vhosts/domain.co.uk/httpdocs
looking for '/var/www/vhosts/domain.co.uk/httpdocs/build.xml' ...
looking for '/var/www/vhosts/domain.co.uk/httpdocs/build.xml' ...
looking for 'build.xml' ...
buildfile 'build.xml' not found.
Build step 'Invoke Phing targets' marked build as failure
Finished: FAILURE
If I run my build.xml on it's own it works fine.
I'm using a custom workspace at the moment, before I tried a symlink from the default workspace to my webroot, when I did that it found the build file but failed when trying to run phing. I know it's a problem with permissions but I'm not sure exactly what.
I'm running this on a plesk web server and have tried adding the jenkins user to the psacln and psaserv groups but that didn't work either.
I use hudson but I think is the same problem.
Provide to ant job the full path (advanced settings)
${WORKSPACE}/buil.xml
Assuming the correct set of jenkins user
RUN_AS_USER=jenkins
Go to the custom workspace and
chown -R jenkins:jenkins myworkspace
if it doesn't work
chmod -R 777 myworkspace
then you will fix later.
I hope it helps.
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
Warning: imagejpeg() [function.imagejpeg]: Unable to open '/home/SITENAME/public_html/files/cache/052f225905c1618003df0c5088aec7a9.jpg' for writing: Permission denied in /home/SITENAME/public_html/concrete/helpers/image.php on line 172
I emptied the cache directory and still no luck, and if I change the permissions on the cache folder then I get another error and I can't use the site at all:
Warning: require_once(Zend/Cache/Backend/File.php) [function.require-once]: failed to open stream: No such file or directory in /home/MYACCOUNT/public_html/concrete/libraries/3rdparty/Zend/Cache.php on line 133
Fatal error: require_once() [function.require]: Failed opening required 'Zend/Cache/Backend/File.php' (include_path='.:/usr/lib/php:/usr/local/lib/php:/home/owen/php') in /home/MYACCOUNT/public_html/concrete/libraries/3rdparty/Zend/Cache.php on line 133
I don't get it? I've never had this problem before.
Sounds like a permissions problem to me, but we can't tell from this end.
If you can FTP (or CD) into that /home/SITENAME/public_html/files/
and see if 'files' is owned by, and has the same permissions as public_html
Then see what permissions they NEED to have for your hosting setup.
Check that directory exists.
Check if web server daemon, most of the time - www-data, has write permissions to that particular directory.
For future reference the problem was the PHP handler. It has been changed to CGI mode (as opposed to DSO) and they turned suEXEC ‘off’ - might be useful for someone down the line.