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 <[email protected]> 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
>
