While read line, awk $line with multiple delimiters
The problem isn't with the value of FS it's this line as pointed to by the error:
f = "Alignments_" $5 ".sam" print > fYou have two statements on one line so either separate them with a ; or a newline:
f = "Alignments_" $5 ".sam"; print > fOr:
f = "Alignments_" $5 ".sam"print > fAs full one liner:
awk -F '[:\t]' 'FNR==NR{n[$1];next}$5 in n{print > ("Alignments_"$5".sam")}'Or as a script file i.e script.awk:
BEGIN { FS="[:\t]" }# read the list of numbers in Tile_Number_ListFNR == NR { num[$1] next}# process each line of the .BAM file# any lines with an "unknown" $5 will be ignored$5 in num { f = "Alignments_" $5 ".sam" print > f}To run in this form awk -f script.awk Tile_Number_List.txt little.sam.
Edit:
The character - is used to represent input from stdin instead of a file with many *nix tools.
command | awk -f script.awk Tile_Number_List.txt -