Commit 5e7f70fb authored by mcariou's avatar mcariou
Browse files

correct lp2300 script

parent 05f1ab64
......@@ -12,10 +12,14 @@
#$ -e /home/mcariou/2021_legio/log/
module load R
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.1 0.1 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
......
#!/bin/bash
#$ -S /bin/bash
## name of the job to follow them
#$ -N runscript34
## name of the queue to be used
#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
#$ -cwd
#$ -V
## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
## the dirs must exist before job is launched
#$ -o /home/mcariou/2021_legio/log/
#$ -e /home/mcariou/2021_legio/log/
/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
## Doesn't accomodate multi query yet
#/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
# fin
#!/bin/bash
#$ -S /bin/bash
## name of the job to follow them
#$ -N runscript3
## name of the queue to be used
#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
#$ -cwd
#$ -V
## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
## the dirs must exist before job is launched
#$ -o /home/mcariou/2021_legio/log/
#$ -e /home/mcariou/2021_legio/log/
/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/lpg2300_prot.fasta ~/2021_legio/out_blastn/
# fin
#!/bin/bash
#$ -S /bin/bash
## name of the job to follow them
#$ -N runscript4
## name of the queue to be used
#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
#$ -cwd
#$ -V
## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
## the dirs must exist before job is launched
#$ -o /home/mcariou/2021_legio/log/
#$ -e /home/mcariou/2021_legio/log/
module load R
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
./4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/lpg2300_prot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
# fin
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