ls6_launcher added

automatic_RAD_pipeline.sh

@@ -92,7 +92,7 @@ $HOME/edirect/esearch -db sra -query $BioProject | efetch --format runinfo |cut
 for A in `cat $BioProject.SRR`;do 
 echo "fastq-dump-orig.2.10.5 $A">>gets;
 done
-ls5_launcher_creator.py -j gets -n gets -a tagmap -e [email protected] -t 12:00:00 -w 24 -q normal
+s2_launcher_creator.py -j gets -n gets -a tagmap -e [email protected] -t 12:00:00 -w 24 -q normal
 getsjob=$(sbatch gets.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 Q= -log10(Perror)*10
@@ -120,25 +120,25 @@ export GENOME_REF=all_cc.fasta
 for file in *.fastq; do
 echo "cutadapt --format fastq -q 15,15 -a AGATCGGA  -m $TagLen -l $TagLen -o ${file/.fastq/}.trim0 $file > ${file}_trimlog.txt && head -12000000 ${file/.fastq/}.trim0 > ${file/.fastq/}.trim && rm ${file/.fastq/}.trim0" >> trim;
 done
-ls5_launcher_creator.py -j trim -n trim -a tagmap -e [email protected] -t 1:00:00 -w 48 -q normal
+s2_launcher_creator.py -j trim -n trim -a tagmap -e [email protected] -t 1:00:00 -w 48 -q normal
 trimjob=$(sbatch trim.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 # converting fastq to fasta (for kmer analysis)
 >f2f
 for F in `ls *fastq`; do echo "paste - - - - < ${F/.fastq/}.trim | cut -f 1,2 | sed 's/^@/>/' | tr \"\t\" \"\n\" > ${F/.fastq/}.fasta" >>f2f ;done
-ls5_launcher_creator.py -j f2f -n f2f -a tagmap -e [email protected] -t 0:05:00 -w 48 -q normal
+s2_launcher_creator.py -j f2f -n f2f -a tagmap -e [email protected] -t 0:05:00 -w 48 -q normal
 f2fjob=$(sbatch --dependency=afterok:$trimjob f2f.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 # analyzing kmers, removing singletons from each file (kmerer.pl)
 >jelly
 for F in `ls *fastq`; do echo "jellyfish count -m $TagLen -s 100M -t 1 -C ${F/.fastq/}.fasta -o ${F/.fastq/}.jf && jellyfish dump ${F/.fastq/}.jf | kmerer.pl - 2 > ${F/.fastq/}.kmers.fa">>jelly;done
-ls5_launcher_creator.py -j jelly -n jelly -a tagmap -e [email protected] -t 0:10:00 -w 24 -q normal
+s2_launcher_creator.py -j jelly -n jelly -a tagmap -e [email protected] -t 0:10:00 -w 24 -q normal
 jellyjob=$(sbatch --dependency=afterok:$f2fjob jelly.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 # merging kmer lists and filtering kmers aiming to get major alleles
 # clustering, concatenating into fake genome (10 chromosomes), and indexing it
 echo "ls *kmers.fa > all.kf && mergeKmers.pl all.kf minDP=10 minInd=5 > kmers.tab && cat kmers.tab | shuf | awk '{print \">\"\$1\"\n\"\$2}' > all.fasta && cd-hit-est -i all.fasta -o all.clust -aL 1 -aS 1 -g 1 -c $MatchFrac -M 0 -T 0 && concatFasta.pl fasta=all.clust num=10 && bowtie2-build all_cc.fasta all_cc.fasta && samtools faidx all_cc.fasta" >mk
-ls5_launcher_creator.py -j mk -n mk -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j mk -n mk -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 mergejob=$(sbatch --dependency=afterok:$jellyjob  mk.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 #mergejob=$(sbatch mk.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
@@ -148,7 +148,7 @@ for F in `ls *.fastq`; do
 REF=all_cc.fasta
 echo "bowtie2 --no-unal -x $REF -U ${F/.fastq/}.trim -S ${F/.fastq/}.sam && samtools sort -O bam -o ${F/.fastq/}.bam ${F/.fastq/}.sam && samtools index ${F/.fastq/}.bam">>maps
 done
-ls5_launcher_creator.py -j maps -n maps -a tagmap -e [email protected] -t 2:00:00 -w 24 -q normal
+s2_launcher_creator.py -j maps -n maps -a tagmap -e [email protected] -t 2:00:00 -w 24 -q normal
 mapsjob=$(sbatch --dependency=afterok:$mergejob  maps.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 # quality assessment, removing bams with log(coverage)<3SD
@@ -158,7 +158,7 @@ FILTERSQ='-uniqueOnly 1 -remove_bads 1 -minMapQ 20 -minInd $MI'
 TODOQ="-doQsDist 1 -doDepth 1 -doCounts 1 -dumpCounts 2"
 echo 'export NIND=`cat bams | wc -l`; export MI=`echo "($NIND*$MinIndPerc+0.5)/1" | bc`' >calc1
 echo "ls *.bam > bams && source calc1 && angsd -b bams -r chr1:1-1000000 -GL 1 $FILTERSQ $TODOQ -P 12 -out dd && Rscript ~/bin/plotQC.R prefix=dd">a0
-ls5_launcher_creator.py -j a0 -n a0 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j a0 -n a0 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 qjob=$(sbatch --dependency=afterok:$mapsjob a0.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 #------------ examine dd.pdf, decide on MinIndPerc and whether bams.qc is reasonable
@@ -173,7 +173,7 @@ FILTERS0='-minInd $MI -uniqueOnly 1 -remove_bads 1 -minMapQ 20 -minQ 20 -snp_pva
 TODO0='-doMajorMinor 1 -doMaf 1 -doCounts 1 -makeMatrix 1 -doIBS 1 -doCov 1 -doPost 1 -doGlf 2'
 echo 'export NIND=`cat bams.qc | wc -l`; export MI=`echo "($NIND*$MinIndPerc+0.5)/1" | bc`' >calc1
 echo "source calc1 && angsd -b bams.qc -GL 1 $FILTERS0 $TODO0 -P 12 -out myresult && Rscript ~/bin/detect_clones.R bams.qc myresult.ibsMat 0.15">a1
-ls5_launcher_creator.py -j a1 -n a1 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j a1 -n a1 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 # a1job=$(sbatch --dependency=afterok:$qjob a1.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 a1job=$(sbatch a1.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
@@ -187,7 +187,7 @@ FILTERS1='-minInd $MI2 -uniqueOnly 1 -remove_bads 1 -minMapQ 20 -minQ 20 -snp_pv
 TODO1='-doMajorMinor 1 -doMaf 1 -doCounts 1 -makeMatrix 1 -doIBS 1 -doCov 1 -doPost 1 -doGlf 2'
 echo 'cat bams.nr | sort > bams.NR && mv bams.NR bams.nr && export NIND2=`cat bams.nr | wc -l`; export MI2=`echo "($NIND2*$MinIndPerc+0.5)/1" | bc`; export MAF=`echo "3/(2*$NIND2)" | bc -l`' >calc2
 echo "source calc2 && angsd -b bams.nr -GL 1 $FILTERS1 $TODO1 -P 12 -out myresult2 && Rscript ~/bin/pcaStructure.R myresult2.ibsMat">a2
-ls5_launcher_creator.py -j a2 -n a2 -a tagmap -e [email protected] -t 2:00:00 -w 1 
+s2_launcher_creator.py -j a2 -n a2 -a tagmap -e [email protected] -t 2:00:00 -w 1 
 -q normal
 a2job=$(sbatch --dependency=afterok:$a1job a2.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 #a2job=$(sbatch  a2.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
@@ -196,7 +196,7 @@ a2job=$(sbatch --dependency=afterok:$a1job a2.slurm | grep "Submitted batch job"
 
 module load python2
 echo 'python ~/pcangsd/pcangsd.py -beagle myresult2.beagle.gz -admix -o pcangsd -inbreed 2 -kinship -selection -threads 12' >adm
-ls5_launcher_creator.py -j adm -n adm -a tagmap -e [email protected] -t 0:10:00 -w 1 -q normal
+s2_launcher_creator.py -j adm -n adm -a tagmap -e [email protected] -t 0:10:00 -w 1 -q normal
 admjob=$(sbatch --dependency=afterok:$a2job adm.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 # ------- genetic diversity stats based on all well-genotyped sites (including invariants)
@@ -209,21 +209,21 @@ FILTERS='-minInd $MI2 -uniqueOnly 1 -skipTriallelic 1 -minMapQ 20 -minQ 20 -doHW
 TODO="-doSaf 1 -anc $REF -ref $GENOME_REF -doMajorMinor 1 -doMaf 1 -dosnpstat 1 -doPost 1 -doGlf 2"
 echo 'export NIND2=`cat bams.nr | wc -l`; export MI2=`echo "($NIND2*$MinIndPerc+0.5)/1" | bc`' >calc2
 echo "source calc2 && angsd -b bams.nr -r chr5 -GL 1 -P 12 $FILTERS $TODO -out chr5 && realSFS chr5.saf.idx -P 12 -fold 1 > chr5.sfs && realSFS saf2theta chr5.saf.idx -outname chr5 -sfs chr5.sfs -fold 1 && thetaStat do_stat chr5.thetas.idx -outnames chr5 && grep \"chr\" chr5.pestPG | awk '{ print \$4/\$14}' >piPerChrom">sfsj
-ls5_launcher_creator.py -j sfsj -n sfsj -t 2:00:00 -e [email protected] -w 1 -a tagmap -q normal
+s2_launcher_creator.py -j sfsj -n sfsj -t 2:00:00 -e [email protected] -w 1 -a tagmap -q normal
 sfsjob=$(sbatch --dependency=afterok:$a1job sfsj.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 #sfsjob=$(sbatch sfsj.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 
 # individual heterozygosities (proportion of heterozygotes across SNPs that pass sfsjob filters)
 echo "Rscript ~/bin/heterozygosity_beagle.R chr5.beagle.gz >indHets" >bg
-ls5_launcher_creator.py -j bg -n bg -a tagmap -e [email protected] -t 12:00:00 -w 1 -q normal
+s2_launcher_creator.py -j bg -n bg -a tagmap -e [email protected] -t 12:00:00 -w 1 -q normal
 sbatch --dependency=afterok:$sfsjob bg.slurm
 # heterozygosity_beagle.R script (by Nathaniel Pope) outputs *_zygosity.RData R data bundle containing AFS (rows) for each individual (columns). The proportion of heterozygotes is the second row. Individual heterozygosities are also printed out to STDOUT (in the case above, saved to text file indHets)
 
 # relatedness with NgsRelate
 echo 'export NIND2=`cat bams.nr | wc -l`; export NS=``zcat g3.mafs.gz | wc -l`' >calc3
 echo 'source calc3 && zcat g3.mafs.gz | cut -f5 |sed 1d >freq && ngsRelate  -g g3.glf.gz -n $NIND -f freq >g3.relatedness' >rel
-ls5_launcher_creator.py -j rel -n rel -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j rel -n rel -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 reljob=$(sbatch rel.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 
@@ -243,13 +243,13 @@ FILTERS1='-minInd $MI2 -uniqueOnly 1 -remove_bads 1 -minMapQ 20 -minQ 20 -snp_pv
 TODO1='-doMajorMinor 1 -doMaf 1 -doCounts 1 -doPost 1 -doGlf 3'
 echo 'cat bams.nr | sort > bams.NR && mv bams.NR bams.nr && export NIND2=`cat bams.nr | wc -l`; export MI2=`echo "($NIND2*$MinIndPerc+0.5)/1" | bc`' >calc2
 echo "source calc2 && angsd -b bams.nr -GL 1 $FILTERS1 $TODO1 -P 12 -out g3">g3
-ls5_launcher_creator.py -j g3 -n g3 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j g3 -n g3 -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 g3job=$(sbatch g3.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
 
 # individual inbreeding coeffs
 echo 'zcat g3.glf.gz | ngsF --glf - --n_ind 44 --n_sites 909052 --out inbr' >nf
-ls5_launcher_creator.py -j nf -n nf -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j nf -n nf -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 ngsFjob=$(sbatch --dependency=afterok:$g3job nf.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 #ngsFjob=$(sbatch nf.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')
 
@@ -258,7 +258,7 @@ zcat g3.mafs.gz | cut -f5 |sed 1d >freq
 # relatedness with NgsRelate
 echo 'export NIND2=`cat bams.nr | wc -l`; export NS=``zcat g3.mafs.gz | wc -l`' >calc3
 echo 'source calc3 && zcat g3.mafs.gz | cut -f5 |sed 1d >freq && ngsRelate  -g g3.glf.gz -n $NIND -f freq >g3.relatedness' >rel
-ls5_launcher_creator.py -j rel -n rel -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
+s2_launcher_creator.py -j rel -n rel -a tagmap -e [email protected] -t 2:00:00 -w 1 -q normal
 reljob=$(sbatch rel.slurm | grep "Submitted batch job" | perl -pe 's/\D//g')