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Merge pull request #260 from telatin/master
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Fix space after backslash [sh: command not found]
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ursky authored Feb 26, 2020
2 parents 2c9fe75 + 1c0455d commit 9039e25
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions bin/metawrap-modules/kraken.sh
Original file line number Diff line number Diff line change
Expand Up @@ -123,8 +123,8 @@ for num in "$@"; do
# shuffle reads, select top N reads, and then restore tabulation, then
# separate reads into F and R files
paste $reads_1 $reads_2 | \
awk '{ printf("%s",$0); n++; if(n%4==0) { printf("\n");} else { printf("\t\t");} }' | \
shuf | head -n $depth | sed 's/\t\t/\n/g' | \
awk '{ printf("%s",$0); n++; if(n%4==0) { printf("\n");} else { printf("\t\t");} }' | \
shuf | head -n $depth | sed 's/\t\t/\n/g' | \
awk -F"\t" '{print $1 > "'"${out}/tmp_1.fastq"'"; print $2 > "'"${out}/tmp_2.fastq"'"}'
reads_1=${out}/tmp_1.fastq
reads_2=${out}/tmp_2.fastq
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