Frequently asked questions
You will find here frequently asked questions, organized by thematics.
Access
Once your account is activated, you can log in different ways.
Terminal
[stage01@migale ~]$ ssh stage01@migale.jouy.inra.fr
Windows
For Windows, you need to use a terminal emulator tool such as MoBaXterm.The only way to change your password is to fill the dedicated form.
If you lost your password, send a mail at help-migale@inra.fr. We will attribute you a new password and then you can change it easyly with the previous link.
If you lost your password, send a mail at help-migale@inra.fr. We will attribute you a new password and then you can change it easyly with the previous link.
Imagine you want to copy the file myfile.txt to the directory /projet/tmp/ on the migale server.
Terminal
[stage01@mylocalhost ~]$ scp myfile.txt stage01@migale.jouy.inra.fr:/projet/tmp/The password will be asked.
For copying a directory, add the -r option after scp
[stage01@mylocalhost ~]$ scp -r mydir stage01@migale.jouy.inra.fr:/projet/tmp/
Windows
For Windows, you need to use a tool such as FileZilla.Conda
[stage01@migale ~]$ conda info --envs # conda environments: # base * /usr/local/genome/Anaconda2-5.1.0 BasicQC /usr/local/genome/Anaconda2-5.1.0/envs/BasicQC abyss-2.2.1 /usr/local/genome/Anaconda2-5.1.0/envs/abyss-2.2.1 admixture-1.3.0 /usr/local/genome/Anaconda2-5.1.0/envs/admixture-1.3.0 amos-3.1.0 /usr/local/genome/Anaconda2-5.1.0/envs/amos-3.1.0 ...
Imagine I want to know the name of the bwa conda environment. I can find it by typing:
[stage01@migale ~]$ conda info --envs | grep bwa bwa-0.7.17 /usr/local/genome/Anaconda2-5.1.0/envs/bwa-0.7.17
To use bwa with conda, you need to activate the bwa environment
[stage01@migale ~]$ conda activate bwa-0.7.17 (bwa-0.7.17) [stage01@migale ~]$ bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.17-r1188 Contact: Heng Li Usage: bwa command [options] Command: index index sequences in the FASTA format mem BWA-MEM algorithm fastmap identify super-maximal exact matches pemerge merge overlapping paired ends (EXPERIMENTAL) aln gapped/ungapped alignment samse generate alignment (single ended) sampe generate alignment (paired ended) bwasw BWA-SW for long queries shm manage indices in shared memory fa2pac convert FASTA to PAC format pac2bwt generate BWT from PAC pac2bwtgen alternative algorithm for generating BWT bwtupdate update .bwt to the new format bwt2sa generate SA from BWT and Occ Note: To use BWA, you need to first index the genome with `bwa index'. There are three alignment algorithms in BWA: `mem', `bwasw', and `aln/samse/sampe'. If you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for the manual.
And to leave conda environment
(bwa-0.7.17) [stage01@migale ~]$conda deactivate [stage01@migale ~]$
To use a conda environment, it is necessary to tell snakemake to load the
.bashrc To do this, add these lines at the beginning of your Snakafile:
shell.executable("/bin/bash")
shell.prefix("source ~/.bashrc;")
In your snakemake rules, you can now use the environments conda with: conda activate my_env. As a reminder, the list of available environments is accessible with:
conda info --envsMore informations here in the Snakemake FAQ.
To use multiple threads, you have to specify it by adding
-pe thread to your submission command.
Example:
[stage01@migale ~]$ qsub -pe thread 8 myscript.sh
The number of threads has to be coherent with the usage of the jobs. If the tool you run is not using multiple threads, you don't need to use this option!
The
Eqw state indicates that your job is in error state. To obtain the reason why, use the qstat command with your job-ID.
Example:
[stage01@migale ~]$ qsub -cwd -V -N myblast -o /out/myblast.stdout -b y "blastn -db subject.fasta -query query.fasta -out /out/out.blast"
Your job 1995192 ("myblast") has been submitted
[stage01@migale ~]$ qstat
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
1995192 0.00000 myblast stage01 Eqw 10/04/2019 17:11:46 1
[stage01@migale ~]$ qstat -j 1995192
...
error reason 1: 10/16/2019 14:35:39 [46342:142027]: error: can't open output file "/out/myblast.stdout": No such file or directory
...
Example> 
[stage01@migale ~]$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 2039350 0.60500 myblast stage01 qw 10/16/2019 14:44:34 100In some cases, jobs are never started and will never be started. In this example, the number of reserved threads is higher than what the nodes offer. As a result, SGE waits until it has a 100-slot node at its disposal to start your job. To check if the waiting is normal, use the qstat command with the job number to check that there is no warning as in this example. You will find here the detail about our resources.
[stage01@migale ~]$ qstat -j 2039350 ... cannot run in PE "thread" because it only offers 0 slots ...
If you leave your session, you can be informed by mail when your jobs are finished using the specific options offered by SGE (command qsub):
-m eaWill send email when job ends or aborts-M <emailaddress>Email address to send email to
watch. Watch is used to run any arbitrary command at regular intervals and displays the output of the command on the terminal window. It is useful when you have to execute a command repeatedly and watch the command output change over time. In this case, the output of qstat will be empty.
[stage01@migale ~]$ watch -n 5 "qstat" # Will run qstat every 5 seconds
When you delete a dataset, it is not really deleted but hidden. It is a security in case of misuse. You can restore them. To delete them permanently, click on the button Delete permanently from disk. The quota will then be updated.
The most common reason why Galaxy cannot build a workflow from a history is that one of the tools used has been updated and parameters have changed. The only solution is to build a worflow from scratch.
If your jobs failed on cluster with this error message:
*** caught illegal operation ***
address 0x2b8c823fb12a, cause 'illegal operand'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath")
../..
We have noticed problems on some nodes of the cluster when using some R libraries.
These problems occur on the oldest nodes because their characteristics no longer allow them to be compatible with these libraries and the version of R.
In order to get around this limitation, we have created a particular group of nodes including only the most recent ones. "@recentNodes"
Here is how to use it:
qsub -q short.q@@recentNodes
The "tar" command allows you to archive several files or the entire contents of a folder in a single file. The "z" parameter requires the tar file to becompressed so that it takes up less disk space
Create tar.gz archive file
[stage01@migale ~]$ tar cvzf archive_name.tar.gz folder_to_archive
Untar and uncompress tar.gz archive file
[stage01@migale ~]$ tar xvfz archive_name.tar.gz
As a matter of habit, we note .tar to indicate that it is an archive and .gz to indicate that the file has been compressed with gzip.
tar usage and options
- c create a archive file
- x extract a archive file
- v show the progress of archive file
- f filename of archive file
- t viewing content of archive file
- j filter archive through bzip2
- z filter archive through gzip
It means you have no space left on current directory and you can not work.
You need to check your data and your work space with commands : df(disk free)and du(disk usage)and delete or archive some data.
[stage01@migale ~]$ df -h /projet/maiage/work/ Filesystem Size Used Avail Use% Mounted on nasproj2:/vs2_maiage_work 17T 17T 0M 100% /projet/maiage/work [stage01@migale ~]$ du -sh ~stage01 14G /projet/maiage/work/stage01And to see details by folder that you use
[stage01@migale ~]$ du -sh ~stage01/* 1,7G /home/maiage/formation/stage02/checkm-genome-1.0.18 8,0K /home/maiage/formation/stage02/checkm_test 8,0K /home/maiage/formation/stage02/checkm_test_results 4,0K /home/maiage/formation/stage02/dir1 12G /home/maiage/formation/stage02/dir2 8,0K /home/maiage/formation/stage02/folder1So you can see where you can reduce your data.