When I ran till the final/4th command, the file only contains "ERROR main:: reads group file". But when I ran the same command on example files, it worked just fine.
Why?
>./ssahaSNP a.fastq Sorbil.fasta -tags 1 > test_ssahaSNP.out
>egrep ALIGN test_ssahaSNP.out | awk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' > alignment-line.dat
>egrep ssaha:SNP test_ssahaSNP.out > test_SNP.dat
>./parse_SNP test_SNP.dat test/alignment-cell_line.dat > test_SNP-parse.out
Why?
>./ssahaSNP a.fastq Sorbil.fasta -tags 1 > test_ssahaSNP.out
>egrep ALIGN test_ssahaSNP.out | awk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' > alignment-line.dat
>egrep ssaha:SNP test_ssahaSNP.out > test_SNP.dat
>./parse_SNP test_SNP.dat test/alignment-cell_line.dat > test_SNP-parse.out