If you are working in LINUX, you can use awk as follows:
awk '$12 ~ /Y/{print "@"$1"_000"$2":"$3":"$4":"$5":"$6"#"$7"/"$8"\n"$9"\n+"$1"_000"$2":"$3":"$4":"$5":"$6"#"$7"/"$8"\n"$10}' s_1_export.txt > s_1_sequence.txt
awk '$12 ~ /Y/{print "@"$1"_000"$2":"$3":"$4":"$5":"$6"#"$7"/"$8"\n"$9"\n+"$1"_000"$2":"$3":"$4":"$5":"$6"#"$7"/"$8"\n"$10}' s_1_export.txt > s_1_sequence.txt
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