... | ... | @@ -1025,6 +1025,63 @@ do |
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echo "$file" >> minced_CRISPR_output.txt
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grep -c 'CRISPR' "$file".txt >> minced_CRISPR_output.txt
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done
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## Based on a discussion with Rob Edwards from UCSD, decided to try out CRISPRdetect-parser
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# from here: https://github.com/hwalinga/crisprdetect-parser
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cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr
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conda activate emboss
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conda install -c bioconda viennarna
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conda install -c anaconda perl
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git clone https://github.com/hwalinga/crisprdetect-parser.git
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cd crisprdetect-parser/CRISPRDetect_2.4_grep_patched
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export PATH=$PATH:/home/users/sbusi/apps/miniconda3/envs/cd-hit/bin # for cd-hit
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export PATH=$PATH:/home/users/sbusi/apps/miniconda3/envs/anvio6/bin # for blastn
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export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin # for perl
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export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl # for perl
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wget http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz
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tar xvzf Parallel-ForkManager-1.19.tar.gz
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cd Parallel-ForkManager-1.19
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perl Makefile.PL PREFIX=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/crisprdetect-parser/CRISPRDetect_2.4_grep_patched/Parallel-ForkManager-1.19
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make test && make install
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####### INSTALLATION NOT WORKING ########
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```
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##### PLASMIDS #####
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- checking the number of plasmids in the assemblies
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```
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# grep -hnr "plasmid" $i_plasflow_prediction_final.tsv > $i_plasmids_selected.tsv
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for file in /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/*final.tsv
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do
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echo $file
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grep -c 'plasmid.' "$file"
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done
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# /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/flye_plasflow_prediction_final.tsv
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# 280
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# /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/megahit_plasflow_prediction_final.tsv
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# 5186
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# /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/metaspades_hybrid_plasflow_prediction_final.tsv
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# 3211
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# /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/metaspades_plasflow_prediction_final.tsv
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# 5718
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# number of contigs used as input:
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# 2533982 flye_filtered.part_001.fna
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# 975951 megahit_filtered.part_001.fna
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# 829650 megahit_filtered.part_002.fna
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# 677918 megahit_filtered.part_003.fna
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# 2483519 total
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# 1992017 metaspades_filtered.part_001.fna
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# 316220 metaspades_filtered.part_002.fna
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# 185613 metaspades_filtered.part_003.fna
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# 2493850 total
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# 2847904 metaspades_hybrid_filtered.part_001.fna
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# 306145 metaspades_hybrid_filtered.part_002.fna
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# 7023 metaspades_hybrid_filtered.part_003.fna
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# 3161072 total
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```
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###############
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... | ... | |