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dramv_annotations
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#!/bin/bash
#SBATCH --nodes=1 # Number of requested nodes
#SBATCH --ntasks=2 # Cores per node requested
#SBATCH --time=7-50:00:00 # Timelimit
#SBATCH --mem=2gb # Job memory (1024gb=1tb)
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH [email protected]
#SBATCH --partition=wrighton-hi,wrighton-low
source /opt/Miniconda2/miniconda2/bin/activate DRAM
cd /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/
#remove bad chars from tab
#RAM-v.py remove_bad_characters -v /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/affi_tab_files_for_dramv/all_huttenhower_virsorter_affi-contigs.tab -o /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/affi_tab_files_for_dramv/all_huttenhower_virsorter_affi-contigs_nobadchars.tab
#remove bad chars from fasta of concatenated viruses ge10kb
DRAM-v.py remove_bad_characters -i /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/ge10kb_viral_fasta_unclustered/all_huttenhower_VIRSorter_cat1245_ge10kb.fasta -o /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/ge10kb_viral_fasta_unclustered/all_huttenhower_VIRSorter_cat1245_ge10kb_nobadchars.fasta
############### Then we annotate after removing bad headers
#!/bin/bash
source /home/rmflynn/miniconda3/bin/activate ame
DRAM-setup.py import_config --config_loc ~/DRAM_CONFIG_20220116
# source /opt/Miniconda2/miniconda2/bin/activate DRAM
cd /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/
#annotate
DRAM-v.py annotate \
-i /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/ge10kb_viral_fasta_unclustered/all_huttenhower_VIRSorter_cat1245_ge10kb_nobadchars.fasta \
-v /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/affi_tab_files_for_dramv/all_huttenhower_virsorter_affi-contigs_nobadchars.tab \
-o /home/projects-wrighton/lloyd-price_data/assemby_renamed_for_virsorter_JRR/dramv_output --min_contig_size 0 --threads 25 &> dramv_no-uniref_log.txt