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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Regarding the fact that what used to be supported by the system now produces errors #16

Open inagaki-s opened 1 year ago

inagaki-s commented 1 year ago

I was executing the command while changing the sample number as follows.

cwltool VIRTUS.PE.cwl \ --fastq1 ../DU_control/S20/S20R1.fastq.gz \ --fastq2 ../DU_control/S20/S20R2.fastq.gz \ --genomeDir_human ../test/STAR_index_human \ --genomeDir_virus ../test/STAR_index_virus \ --outFileNamePrefix_human S20 \ --nthreads 40

However, after closing the Ubuntu tab once, I get the following error when I type the same command, and I don't know how to fix it. I would appreciate it if you could provide me with a solution.

”error cord” INFO /home/tebio/.local/bin/cwltool 3.1.20210922203925 INFO Resolved 'VIRTUS.PE.cwl' to 'file:///mnt/c/Ubuntu/VIRTUS/VIRTUS2/workflow/VIRTUS.PE.cwl' ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information. The error was: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim

yyoshiaki commented 1 year ago

The error you are encountering is because cwltool requires the Node.js engine to evaluate and validate JavaScript expressions, but it cannot find it. Please make sure that Node.js is installed and properly configured on your system.

If you don't have Node.js installed, you can follow these steps to install it:

Open your terminal. Run the following command to add the necessary repository for installing Node.js:

curl -sL https://deb.nodesource.com/setup_14.x | sudo -E bash -

To install Node.js, execute the following command:

sudo apt-get install -y nodejs

After the installation is complete, run the following command to check the version of Node.js:

node -v

Once you have verified that Node.js is correctly installed, try running the cwltool command again. If the problem still persists, make sure that the path is set correctly. You can find the directory where Node.js is installed by running the following command:

which node

Next, you need to add the path to Node.js to the environment variable PATH. For example, if Node.js is installed at /usr/local/bin/node, you can run the following command to add the path:

export PATH=$PATH:/usr/local/bin

This should enable cwltool to detect Node.js. Run the cwltool command again and check if the issue is resolved.