Error in bash with unary operator in complicated loop

Asked Aug 10 '20 at 15:02

Active Aug 10 '20 at 15:08

Viewed 28 times

I cannot understand, what is wrong with my code. I try to print out file items in subdirectory (in special order). But I receive error

./testDir.sh: line 23: [: : unary operator expected
cut: the delimiter must be a single character

#!/bin/bash
#PBS -N printing subdirectories job2
#PBS -j oe
#PBS -A rsu
INPATH=/home/groups/covid-19/seq_reads/MGI/V300042154
cd $INPATH
for dir in */; do
  for file in $dir/*.fq.gz; do
    for file2 in $dir.fq.gz; do
      bname1=$(basename $file1 '.fq.gz')
      sample1="$( cut -d'_'-f 1,2,3<<<"$bname1")"
      read1="$( cut -d'_' -f 4 <<<"$bname1")"
      bname2=$(basename $file2 '.fq.gz')
      sample2="$( cut -d'_'-f 1,2,3<<<"$bname2")"

      if [ "$sample1" == "$sample2"]&&["$read1" != "$read2"]&&["$read1" == 1 ]; then
        echo "$sample1""$sample2""$read1""read2"
        #Here Trimmomatic should be started
      else
        true
      fi
    done
  done
done

edited Aug 10 '20 at 15:08

Brian61354270

8,690
4
21
43

asked Aug 10 '20 at 15:02

hurricane2923

4

Spaces around `]` are mandatory. Also, please indent the code. – choroba Aug 10 '20 at 15:04
Algorithm himself seems more complicated than needed ; even it is depending on your needs. – francois P Aug 10 '20 at 15:11
Thanks! I corrected spaces around [ ]. However, the problem remains with cut: the delimiter must be a single character – hurricane2923 Aug 10 '20 at 16:51
my files consist of Vhwhewjjde_L0n_nnn_1.fq.gz – hurricane2923 Aug 10 '20 at 16:53
Check your `cut`s -- two have no space after `cut -d' '`, and so are just considered one long broken argument to cut. – l3l_aze Aug 12 '20 at 16:16

Error in bash with unary operator in complicated loop

0 Answers0