This is a test version of Biostars. For the public version, visit https://www.biostars.org.
basename: extra operand error

I want to use an array for fastq files:-

RUN=${SLURM_ARRAY_TASK_ID}
R1=$(head -n $RUN input.txt | tail -n 1)
data=$(basename $R1 | cut -f 1 -d'_')

Where, input.txt:

GC-1   9  27
GC-2   7  79
GC-3   2  53
GC-4   6  32

I am getting an error $data: basename: extra operand '27'

I am not sure where is the error. Thank you!

sequence
• 2,499 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by evelyn evelyn

the message is clear. there is more tokens than basename wants in the output of head -n $RUN input.txt | tail -n 1

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Have you looked on StackExchange? Pure unix questions like this can often be answered by checking around there.

• 0 views • link
written by GenoMax GenoMax

Hello evelyn!

We believe that this post does not fit the main topic of this site.

what genomax said. Not related to bioinformatics.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

0 answers

No answers yet.

Log in to answer this question.

More posts like this