diff --git a/20200810_mapping_on_d427_hybridAB.sh b/20200810_mapping_on_d427_hybridAB.sh
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+++ b/20200810_mapping_on_d427_hybridAB.sh
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+
+#create index
+bowtie2-build -f /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB/d427_hybrid_contigs_new_names.fasta /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB
+
+
+
+bowtie2 --local -x /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB -X 5000 --very-sensitive-local -k 50 -p 4 --phred33 -1 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/31C_L1_non_aligned_R1.fastq -2 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/31C_L1_non_aligned_R2.fastq -S /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/31C_map_on_d427_hybridAB.sam
+
+paste - - - - - - - - < 32C_L1_non_aligned.fastq  \
+    | tee >(cut -f 1-4 | tr "\t" "\n" > 32C_L1_non_aligned_R1.fastq ) \
+    | cut -f 5-8 | tr "\t" "\n" > 32C_L1_non_aligned_R2.fastq 
+
+bowtie2 --local -x /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB -X 5000 --very-sensitive-local -k 50 -p 4 --phred33 -1 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/32C_L1_non_aligned_R1.fastq -2 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/32C_L1_non_aligned_R2.fastq -S /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/32C_map_on_d427_hybridAB.sam
+
+paste - - - - - - - - < 33C_L1_non_aligned.fastq  \
+    | tee >(cut -f 1-4 | tr "\t" "\n" > 33C_L1_non_aligned_R1.fastq ) \
+    | cut -f 5-8 | tr "\t" "\n" > 33C_L1_non_aligned_R2.fastq 
+
+bowtie2 --local -x /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB -X 5000 --very-sensitive-local -k 50 -p 4 --phred33 -1 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/33C_L1_non_aligned_R1.fastq -2 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/33C_L1_non_aligned_R2.fastq -S /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/33C_map_on_d427_hybridAB.sam
+
+'Warning: Output file '/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/31C_map_on_uniref90.bam' was specified without -S.  This will not work in future Bowtie 2 versions.  Please use -S instead.
+Could not locate a Bowtie index corresponding to basename "/media/bioinfoteam/SCRATCH_850GB/databases/uniref90"
+Error: Encountered internal Bowtie 2 exception (#1)
+Command: /home/bioinfoteam/anaconda3/envs/bowtie_env/bin/bowtie2-align-s --wrapper basic-0 --local -x /media/bioinfoteam/SCRATCH_850GB/databases/uniref90 -X 5000 --very-sensitive-local -k 50 -p 4 --phred33 -1 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/31C_L1_non_aligned_R1.fastq -2 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non_aligned/31C_L1_non_aligned_R2.fastq -b /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/31C_map_on_uniref90.bam 
+(ERR): bowtie2-align exited with value 1'
+