Loading CPU/juicer.sh +4 −4 Changes for CPU/juicer.sh: 4 added lines, 4 removed lines. Original line number Diff line number Diff line Loading @@ -367,8 +367,8 @@ then # Align read1 if [ -n "$shortread" ] || [ "$shortreadend" -eq 1 ] then echo "Running command bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam" bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam echo "Running command bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam" bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam if [ $? -ne 0 ] then echo "***! Alignment of $name1$ext failed." Loading @@ -390,8 +390,8 @@ then # Align read2 if [ -n "$shortread" ] || [ "$shortreadend" -eq 2 ] then echo "Running command bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam " bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam echo "Running command bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam " bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam if [ $? -ne 0 ] then echo "***! Alignment of $name2$ext failed." Loading Loading
CPU/juicer.sh +4 −4 Changes for CPU/juicer.sh: 4 added lines, 4 removed lines. Original line number Diff line number Diff line Loading @@ -367,8 +367,8 @@ then # Align read1 if [ -n "$shortread" ] || [ "$shortreadend" -eq 1 ] then echo "Running command bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam" bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam echo "Running command bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam" bwa aln -q 15 $threadstring $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam if [ $? -ne 0 ] then echo "***! Alignment of $name1$ext failed." Loading @@ -390,8 +390,8 @@ then # Align read2 if [ -n "$shortread" ] || [ "$shortreadend" -eq 2 ] then echo "Running command bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam " bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam echo "Running command bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam " bwa aln -q 15 $threadstring $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam if [ $? -ne 0 ] then echo "***! Alignment of $name2$ext failed." Loading
