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YuuMJ 2025-06-01 16:10:31 +08:00
commit bf98a68bff
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20
2_assembly/Saccharomyces_cerevisiae_spades_ymj.pbs Normal file
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#PBS -N Saccharomyces_cerevisiae_spades_ymj
#PBS -l nodes=1:ppn=48
#PBS -r y
#PBS -q promax_yuu
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/2_assembly
echo Start Time is `date`
source activate spades
spades.py --sc -t 48 -m 200 \
-1 ../1_trim/SRR30661791_1_p.fastq \
-2 ../1_trim/SRR30661791_2_p.fastq \
-o spades
conda deactivate
echo End Time is `date`

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3_decontamination/1_Sacc_cerevisiae_dec_bac_ymj.pbs Normal file
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#PBS -N Sacc_cerevisiae_dec_bac_ymj
#PBS -l nodes=1:ppn=48
#PBS -r y
#PBS -q master_431
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/3_decontamination/
echo Start Time is `date`
blastn -db /home/Data_01/share_databases/ncbi_genome_refseq_bac_old/ncbi_genome_refseq_bac_old \
-query /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/2_assembly/spades/scaffolds.fasta \
-out Sacc_cerevisiae_dec_bac.tab \
-outfmt "6 qseqid qlen sseqid slen pident qcovs qstart qend sstart send mismatch gapopen evalue bitscore" \
-evalue 1e-5 -max_target_seqs 1 -num_threads 48
sed -i '1i\tquery ID\tquery sequence length\tsubject ID\tsubject qequence length\tpercent identities\tcoverage\tqstart\tqend\tsstart\tsend\tmismatch\tgapopen\tevalue\tbitscores ' Sacc_cerevisiae_dec_bac.tab
echo End Time is `date`

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3_decontamination/2_Sacc_cerevisiae_dec_bac_hum_ymj.pbs Normal file
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#PBS -N Saccharomyces_cerevisiae_dec_bac_hum_ymj
#PBS -l nodes=1:ppn=48
#PBS -r y
#PBS -q master_431
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/3_decontamination/
echo Start Time is `date`
blastn -db /home/Data_01/share_databases/human_genome_new/GCA_021234545.1_HCC1395BL_v1.0_genomic_db \
-query Sacc_cerevisiae_dec_bac.fasta \
-out Sacc_cerevisiae_dec_bac_hum.tab \
-outfmt "6 qseqid qlen sseqid slen pident qcovs qstart qend sstart send mismatch gapopen evalue bitscore" \
-evalue 1e-5 -max_target_seqs 1 -num_threads 48
sed -i '1i\tquery ID\tquery sequence length\tsubject ID\tsubject qequence length\tpercent identities\tcoverage\tqstart\tqend\tsstart\tsend\tmismatch\tgapopen\tevalue\tbitscores ' Sacc_cerevisiae_dec_bac_hum.tab
echo End Time is `date`

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3_decontamination/3_Sacc_cerevisiae_dec_bac_hum_geno_rna_ymj.pbs Normal file
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#PBS -N 3_Sacc_cerevisiae_dec_bac_hum_geno_rna_ymj
#PBS -l nodes=1:ppn=48
#PBS -r y
#PBS -q master_431
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/3_decontamination/
echo Start Time is `date`
blastn -db /home/Data_01/share_databases/human_genome_new/GCF_000001405.39_GRCh38.p13_rna_db \
-query 2_Sacc_cerevisiae_dec_bac_hum.fasta \
-out 3_Sacc_cerevisiae_dec_bac_hum_geno_rna.tab \
-outfmt "6 qseqid qlen sseqid slen pident qcovs qstart qend sstart send mismatch gapopen evalue bitscore" \
-evalue 1e-5 -max_target_seqs 1 -num_threads 48
sed -i '1i\tquery ID\tquery sequence length\tsubject ID\tsubject qequence length\tpercent identities\tcoverage\tqstart\tqend\tsstart\tsend\tmismatch\tgapopen\tevalue\tbitscores ' 3_Sacc_cerevisiae_dec_bac_hum_geno_rna.tab
echo End Time is `date`

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3_decontamination/5_Sacc_cerevisiae_cdhit_ymj.pbs Normal file
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#PBS -N 5_Sacc_cerevisiae_cdhit_ymj
#PBS -l nodes=1:ppn=48
#PBS -r y
#PBS -q master_431
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/3_decontamination/
echo Start Time is `date`
cd-hit-est -i 4_Sacc_cerevisiae_dec_all_cov1.fasta -o 5_Sacc_cerevisiae_dec_all_cov1_cdhit.fasta -c 0.9 -n 8 -d 0 -M 32000 -T 48
echo End Time is `date`

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4_prediction/Sacc_cerevisiae_augustus_ymj.pbs Normal file
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#PBS -N Sacc_cerevisiae_augustus_ymj
#PBS -l nodes=1:ppn=8
#PBS -r y
#PBS -q master_431
cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/4_prediction
echo Start Time is `date`
source activate augustus
augustus --progress=true --protein=on --introns=on --start=on --stop=on --cds=on --codingseq=on --gff3=on --species=tetrahymena --extrinsicCfgFile=/home/Data_01/yizhenzhen06/miniconda3/envs/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg ../3_decontamination/5_Sacc_cerevisiae_dec_all_cov1_cdhit.fasta --outfile=Sacc_cerevisiae.gff3
conda deactivate
echo End Time is `date`