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metatran_LBE/20200810_mapping_on_d427_hybridAB.sh
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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
# on file 31
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
# on file 32
# after sortmerna files R1 and R2 are grouped (interleaved)
##bowtie cannot handle interleaved files, need to separate R1 and R2
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
# on file 33
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
##get an error message when try to align against a protein database
##bowtie2 can be use only with nucleotidic database
'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'
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