Re: Parallel not running

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Petty sure something is messing with your PATH environment variable.

Start a new terminal

Run this command:

which parallel

The output will be something like 

/usr/bin/parallel

or nothing at all, in which case you might try

whereis parallel

Add the output from that (maybe /usr/bin) to your PATH

PATH=/usr/bin:${PATH}

Do your work and if you see the same result “not found”, re-fix your PATH

The bigger question is what is altering your PATH

On Mar 30, 2019, at 9:07 AM, Wang Shaopu <spwang0920@hotmail.com> wrote:

Hi, 

May I ask a question? when I run the following command with shell in Linux, the parallel worked. However, after running two times, it did not work anymore with error “parallel: command not found”.

parallel -j 1 --link 'kneaddata -i {1} -i {2} -o kneaddata_out/ \

-db /home/shared/bowtiedb/GRCh38_PhiX --trimmomatic /usr/local/prg/Trimmomatic-0.36/ \

-t 4 --trimmomatic-options "SLIDINGWINDOW:4:20 MINLEN:50" \

--bowtie2-options "--very-sensitive --dovetail" --remove-intermediate-output' \

::: raw_data/*_R1.fastq ::: raw_data/*_R2.fastq

What's the problem? If the parallel is not installed yet, why can it be run at beginning?

Thank you very much.

Best regards,

Wang