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- Check Eoulsan path:
$ which eoulsan.sh- Check Eoulsan version:
$ eoulsan.sh –-version- Use the
infocommand of Eoulsan (2.3 and greater)
# Without workflow file
$ eoulsan.sh info
# With workflow file
$ eoulsan.sh info workflow.xml=== Eoulsan Error ===
Error while executing eoulsan: For the step step1whitelist data generated by the port output already exists: /home/user/Eoulsan_demo/step1whitelist_output/step1whitelist_output_umiwhitelist_T1test.txt
This is not really an error, but rather an advice. If you really want to build an other design file, you may:
- rename the previous design.txt file (i.e. design-old.txt)
- change output directory
- remove file
=== Eoulsan Error ===
Error while executing eoulsan: For the step step1whitelist data generated by the port output already exists: /home/user/Eoulsan_demo/step1whitelist_output/step1whitelist_output_umiwhitelist_T1test.txt
Same as above, but Eoulsan will stop if you don't fix this.
=== Eoulsan Error ===
Error while executing eoulsan: java.io.IOException: Unknown Design format
Check that you properly enter (in this order) eoulsan.sh exec workflow.xml design.txt (and not something like eoulsan.sh exec design.txt workflow.xml). The order in which you write the arguments will prevent Eoulsan from working if not correct.
=== Eoulsan Error ===
Error while normalizing expression data: Rscript -e Sweave("Eoulsan_demo/normalization_output/normalization_exp1.Rnw", output="normalization_exp1.tex")
You may have a problem with R installation. Please run these commands and then try running a second time:
$ sudo R
> source("http://bioconductor.org/biocLite.R")
> biocLite("DESeq")
> install.packages("FactoMineR")=== Eoulsan Error ===
unknown input port name: whitelist
A “port” means an input. Check if the Dataformat whitelist exists, and if yes, check it's ID in the Dataformat file, in the Galaxytool(s) that need(s) this type of input, and paths to the Dataformat in the configuration file.
=== Eoulsan Error ===
Unable to to pull Docker image: genomicpariscentre/newImage
- Check the id/name of your docker image in the workflow file
- Check the galaxytool: in the line, check the name newImage is written the same as in the workflow file.
- Have you pulled you Docker image to genomicpariscentre ? Check also the tags [LINK]. You could try i.e. or .
=== Eoulsan Error ===
Error while executing eoulsan: The "input" port (annotation_gff format) of step "gfffastagenerator" is not linked
This error is due to either not providing the right gff file or not providing the genome fasta file.
- Check that you provided the right genome fasta file and it's path is written in the design file.
- Same with gff file
=== Eoulsan Error ===
Cannot run program "xxx/STAR/2.5.2b/STAR" (in directory "xxx"): error=13, Permission non accordée
If the path where you run eoulsan if not executable, you may encounter some right permissions issues. If that's the case, you can add to your configuration file (i.e. conf.txt): main.executables.tmp.dir=/executable/path
Then run eoulsan adding this new information with the following command:
$ eoulsan -conf conf.txt exec workflow.xml design.txt=== Eoulsan Error ===
Error while executing eoulsan: The "additionalannotation" port (additional_annotation_tsv format) of step "step12singlecellexperiment" is not linked
This message refers to an additional annotation file you may use when building a R SingleCellExperiment object ("step12singlecellexperiment"). You have the possibility to add any information available in BioMart (https://www.ensembl.org/biomart/martview/). Select all what you need and extract the information to a TSV file (select the options you need, click on "results", and then "go"). Eoulsan will add those data directly to the output (SingleCellExperiment object).
In case you do not have any additional annotation file, you can just add AdditionalAnnotationFile=/dev/null in the design file ("Header" section). You can also set the "use.gene.annotation" parameter (in the workflow file) to "false".