for i in 0hrep1-15mMm1kIntron.bam do echo $i # add MD flags for bowtie format # /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.max-intron-1k >& /dev/null > foo.bam2 /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.tr-with-1k-introns.fa >& /dev/null > foo.bam2 samtools view -h foo.bam2 | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk > $i.md.bt mv foo.bam2 $i.md.bam done export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib gcc omit-reads.c -lJudy -o omit-reads time ./omit-reads /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/t/0hrep1-15mMm1kIntron.bam.md.bt nlines 114813970 maxlen 219 n_aligned_reads 11481540 chunksize 1148154 last chunk 10/data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/t/0hrep1-15mMm1kIntron.bam.md.bt-1 cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/ ./myp-all-1kIntrons-saturation-0hrep1.sh &> ./myp-all-1kIntrons-saturation-0hrep1.log & ln -s sh-clusters-6hrep1.txt2-1kIntrons.csv sh-clusters-6hrep1.txt2-1kIntrons-0.csv ./saturation-plots1.sh /data/images/proton/DKlab/mr/parclip/paralyzer/omit-reads ]0;/data/images/proton/DKlab/mr/parclip/paralyzerreczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer$ time ./a.out /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt reading /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt nlines 56882775 maxlen 220 n_aligned_reads 5688393 chunksize 568839 last chunk 10/data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-1 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-2 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-3 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-4 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-5 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-6 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-7 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-8 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-9 real 2m34.961s user 2m2.124s sys 0m31.296s wc /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt* 56882775 455062178 7252735073 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt 5688283 45506264 724853224 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-1 11376602 91012812 1452670833 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-2 17064928 136519419 2180045847 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-3 22753284 182026264 2907961747 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-4 28441598 227532775 3636172619 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-5 34129886 273039078 4364103237 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-6 39818148 318545172 5089327367 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-7 45506507 364052043 5811041548 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-8 51194506 409556029 6531759665 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt-9 time ./a.out /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IL4-15mMm1kIntron.bam.md.bt gcc omit-reads.c -lJudy -o omit-reads /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/myp-all-1kIntrons-saturation1.sh ./saturation-plots2.sh 0h.txt2-1kIn gnuplot> plot "saturation-IFN.txt" f(x)=m*x+c fit f(x) "saturation-IFN.txt" via m,c fit f(x) "saturation-IFN.txt" via m,c After 5 iterations the fit converged. final sum of squares of residuals : 3.49152e+08 rel. change during last iteration : -8.6115e-09 degrees of freedom (FIT_NDF) : 6 rms of residuals (FIT_STDFIT) = sqrt(WSSR/ndf) : 7628.37 variance of residuals (reduced chisquare) = WSSR/ndf : 5.81921e+07 Final set of parameters Asymptotic Standard Error ======================= ========================== m = 1592.02 +/- 89.9 (5.647%) c = -22465.2 +/- 5242 (23.33%) plot "saturation-IFN.txt" ,f(x) q(x)=a*x*x+b*x+c1 fit q(x) "saturation-IFN.txt" via a,b,c1 resultant parameter values a = 8.4557 b = 640.753 c1 = -3651.29 After 7 iterations the fit converged. final sum of squares of residuals : 9.17536e+06 rel. change during last iteration : -1.31675e-08 degrees of freedom (FIT_NDF) : 5 rms of residuals (FIT_STDFIT) = sqrt(WSSR/ndf) : 1354.65 variance of residuals (reduced chisquare) = WSSR/ndf : 1.83507e+06 Final set of parameters Asymptotic Standard Error ======================= ========================== a = 8.4557 +/- 0.6212 (7.347%) b = 640.753 +/- 71.69 (11.19%) c1 = -3651.29 +/- 1666 (45.64%) plot "saturation-IFN.txt" ,f(x),q(x) set xtics format "%.0f" plot "saturation-IFN.txt" ./myp-all-1kIntrons-saturation-6hrep1.sh &> ./myp-all-1kIntrons-saturation-6hrep1.log & reading /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt nlines 222931180 maxlen 221 n_aligned_reads 22293451 chunksize 2229345 cat /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0hrep1-15mMm1kIntron.bam.md.bt /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0hrep2-15mMm.bam.md.bt /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0hrep3-15mMm1kIntron.bam.md.bt > /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h.bt ./omit-reads /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt reading /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/myp-all-1kIntrons-saturation-0h2.sh &> myp-all-1kIntrons-saturation-0h.log2 & ./myp-all-1kIntrons-saturation-0h.sh &> myp-all-1kIntrons-saturation-0h.log ERR more than 223000000 lines nlines 223000000 maxlen 220 n_aligned_reads 33231745 chunksize 3323174 ./omit-reads /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt reading /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt nlines 337745150 maxlen 221 n_aligned_reads 33774991 chunksize 3377499 last chunk 10/data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-1 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-2 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-3 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-4 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-5 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-6 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-7 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-8 /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt-9 set xlabel "0.1 * percent of reads" set ylabel "number of clusters" set grid set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.9.png";plot "sat-0h.txt2-1kIntrons-0.9.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.99.png";plot "sat-0h.txt2-1kIntrons-0.99.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.999.png";plot "sat-0h.txt2-1kIntrons-0.999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.9999.png";plot "sat-0h.txt2-1kIntrons-0.9999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.99999.png";plot "sat-0h.txt2-1kIntrons-0.99999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.999999.png";plot "sat-0h.txt2-1kIntrons-0.999999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.9999999.png"; plot "sat-0h.txt2-1kIntrons-0.9999999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.99999999.png"; plot "sat-0h.txt2-1kIntrons-0.99999999.txt" w l;set term x11;replot set terminal png font 'DejaVuSans' 16 size 1024,768 set output "sat-0h.txt2-1kIntrons-0.999999999.png"; plot "sat-0h.txt2-1kIntrons-0.999999999.txt" w l;set term x11;replot