I am trying to use Trimmomatic and Bowtie2 on a sample (metagenomic) to do some quality filtering and contaminant screening, the sample has been stitched. when I try to run the parallel command on my stitched read I receive this funny warning:
Input is read from the terminal. You either know what you are doing (in which case: YOU ARE AWESOME!) or you forgot ::: or :::: or to pipe data into parallel. If so consider going through the tutorial: man parallel_tutorial. Press CTRL+D to exit
Here is what I am working with:
parallel -j 1 --link 'kneaddata -i {} -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' \ ::: stitched_reads/*.assembled.fastq
Is this normal? is there anything I am doing wrong or is it still working and just showing this warning message? I am new to bioinformatics and using a script to help me run the analysis, I did not make this code myself and have no experience using GNU parallel.
1 answer
You are using the \ incorrectly and that generates an incorrect invocation for the command.
Example:
parallel echo {} ::: A B C
prints:
A
B
C
if I write:
parallel echo {} \ ::: A B C
then it prints:
parallel: Warning: Input is read from the terminal. You are either an expert
parallel: Warning: (in which case: YOU ARE AWESOME!) or maybe you forgot
parallel: Warning: ::: or :::: or -a or to pipe data into parallel. If so
parallel: Warning: consider going through the tutorial: man parallel_tutorial
parallel: Warning: Press CTRL-D to exit.
In the latter case, the continuation character makes the command look like the colons are part of the command.
parallel echo {}::: A B C
It needs a space to separate the colons from the command.
Interesting, indeed not quite the same. Though I admit I find it quite hard to explain why this works (two spaces on each side of \):
parallel echo {} \ ::: A B C
but this does not (one space on each side of the \)
parallel echo {} \ ::: A B C
I thought I grokked Unix :-(
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what is link doing here? and probably, due to escaping input
\ :::there is an error, if I understand correct. It would to understand better, if you could post more details.Try following and check the output:
If every thing looks okay from dummy run, remove '--dry-run'. Check your thread options as well. You are giving 1 thread to parallel and 4 threads to the program. It seems you are using multiple
\in code. Are you running in multiple lines or in a single line?In addition to what cpad0112 said, you don't really need GNU parallel for this since
-j 1means you are only using one process.