Note: global and local outputs would be the same, since sequence length is shorter than bp-interaction lengnth. cd /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/; RNAplfold -W 200 -L 150 -u 9 < /tmp/6963270.1.websrv1.q/tmpdhiuqvr4 b'' b'WARNING: window size 200 larger than sequence length 100\n' Warning in calling call_RNAfold: b'' b'WARNING: window size 200 larger than sequence length 100\n' snp_locs: [] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/' --prefix 'RNA-WILDTYPE-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA_dp.ps' --title 'RNA-WILDTYPE' tmpdir is: /tmp/6963270.1.websrv1.q/tmp079gsyg3/ ['/tmp/6963270.1.websrv1.q/tmp079gsyg3/data/sequence.txt', '/tmp/6963270.1.websrv1.q/tmp079gsyg3/data/circos.sequence.txt', '/tmp/6963270.1.websrv1.q/tmp079gsyg3/data/circos.karyotype.txt', '/tmp/6963270.1.websrv1.q/tmp079gsyg3/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**="RNA-WILDTYPE-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmp079gsyg3//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmp079gsyg3//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 2.27s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 2.35s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 2.35s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**=RNA-WILDTYPE-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmp079gsyg3//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmp079gsyg3//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 2.35s guessing configuration file debuggroup summary 2.40s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 3.81s debug will appear for these features: output,summary debuggroup summary 3.81s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-WILDTYPE-circos.png debuggroup summary 3.81s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-WILDTYPE-circos.svg debuggroup summary 3.85s parsing karyotype and organizing ideograms debuggroup summary 3.85s karyotype has 1 chromosomes of total size 101 debuggroup summary 3.86s applying global and local scaling debuggroup summary 3.86s allocating image, colors and brushes debuggroup summary 18.73s drawing 1 ideograms of total size 101 debuggroup summary 18.73s drawing highlights and ideograms debuggroup summary 18.76s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 18.78s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt debuggroup summary 18.92s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 18.93s process track_0 link /tmp/6963270.1.websrv1.q/tmp079gsyg3//data/circos.bplinks.txt debuggroup summary 19.24s drawing link track_0 z 50 debuggroup output 20.01s generating output debuggroup output 20.76s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-WILDTYPE-circos.png (210 kb) debuggroup output 20.84s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-WILDTYPE-circos.svg (125 kb) =============================== cd /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/; RNAplfold -W 200 -L 150 -u 9 < /tmp/6963270.1.websrv1.q/tmpwputqht0 b'' b'WARNING: window size 200 larger than sequence length 100\n' Warning in calling call_RNAfold: b'' b'WARNING: window size 200 larger than sequence length 100\n' snp_locs: [19] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/' --prefix 'RNA-MUTANT-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT_dp.ps' --title 'RNA-MUTANT' tmpdir is: /tmp/6963270.1.websrv1.q/tmpma1a92z3/ ['/tmp/6963270.1.websrv1.q/tmpma1a92z3/data/sequence.txt', '/tmp/6963270.1.websrv1.q/tmpma1a92z3/data/circos.sequence.txt', '/tmp/6963270.1.websrv1.q/tmpma1a92z3/data/circos.karyotype.txt', '/tmp/6963270.1.websrv1.q/tmpma1a92z3/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**="RNA-MUTANT-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmpma1a92z3//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmpma1a92z3//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 1.28s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 1.35s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 1.35s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**=RNA-MUTANT-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmpma1a92z3//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmpma1a92z3//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 1.35s guessing configuration file debuggroup summary 1.35s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 1.94s debug will appear for these features: output,summary debuggroup summary 1.95s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-circos.png debuggroup summary 1.95s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-circos.svg debuggroup summary 1.97s parsing karyotype and organizing ideograms debuggroup summary 1.98s karyotype has 1 chromosomes of total size 101 debuggroup summary 1.98s applying global and local scaling debuggroup summary 1.98s allocating image, colors and brushes debuggroup summary 5.43s drawing 1 ideograms of total size 101 debuggroup summary 5.43s drawing highlights and ideograms debuggroup summary 5.43s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 5.44s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt debuggroup summary 5.54s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 5.55s process track_0 link /tmp/6963270.1.websrv1.q/tmpma1a92z3//data/circos.bplinks.txt debuggroup summary 5.92s drawing link track_0 z 50 debuggroup output 6.86s generating output debuggroup output 7.46s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-circos.png (218 kb) debuggroup output 7.58s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-circos.svg (151 kb) =============================== min_max is [-1, 89] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/' --prefix 'RNA-MUTANT-weakened-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT_dp_diff_weakened.dp' --title 'RNA-MUTANT-weakened' tmpdir is: /tmp/6963270.1.websrv1.q/tmpj0cy_lka/ ['/tmp/6963270.1.websrv1.q/tmpj0cy_lka/data/sequence.txt', '/tmp/6963270.1.websrv1.q/tmpj0cy_lka/data/circos.sequence.txt', '/tmp/6963270.1.websrv1.q/tmpj0cy_lka/data/circos.karyotype.txt', '/tmp/6963270.1.websrv1.q/tmpj0cy_lka/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**="RNA-MUTANT-weakened-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmpj0cy_lka//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmpj0cy_lka//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 0.77s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 0.83s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 0.83s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**=RNA-MUTANT-weakened-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmpj0cy_lka//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmpj0cy_lka//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 0.83s guessing configuration file debuggroup summary 0.83s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 1.31s debug will appear for these features: output,summary debuggroup summary 1.31s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-weakened-circos.png debuggroup summary 1.31s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-weakened-circos.svg debuggroup summary 1.34s parsing karyotype and organizing ideograms debuggroup summary 1.34s karyotype has 1 chromosomes of total size 101 debuggroup summary 1.34s applying global and local scaling debuggroup summary 1.34s allocating image, colors and brushes debuggroup summary 4.83s drawing 1 ideograms of total size 101 debuggroup summary 4.83s drawing highlights and ideograms debuggroup summary 4.83s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 4.85s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt debuggroup summary 4.96s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 4.96s process track_0 link /tmp/6963270.1.websrv1.q/tmpj0cy_lka//data/circos.bplinks.txt debuggroup summary 5.14s drawing link track_0 z 50 debuggroup output 5.62s generating output debuggroup output 6.25s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-weakened-circos.png (184 kb) debuggroup output 6.35s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-weakened-circos.svg (75 kb) =============================== cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/' --prefix 'RNA-MUTANT-increased-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT_dp_diff_increased.dp' --title 'RNA-MUTANT-increased' tmpdir is: /tmp/6963270.1.websrv1.q/tmp2emwu1ed/ ['/tmp/6963270.1.websrv1.q/tmp2emwu1ed/data/sequence.txt', '/tmp/6963270.1.websrv1.q/tmp2emwu1ed/data/circos.sequence.txt', '/tmp/6963270.1.websrv1.q/tmp2emwu1ed/data/circos.karyotype.txt', '/tmp/6963270.1.websrv1.q/tmp2emwu1ed/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**="RNA-MUTANT-increased-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmp2emwu1ed//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmp2emwu1ed//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 1.40s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 1.46s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 1.46s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/ -param image/file**=RNA-MUTANT-increased-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963270.1.websrv1.q/tmp2emwu1ed//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt -param links/link/file=/tmp/6963270.1.websrv1.q/tmp2emwu1ed//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 1.46s guessing configuration file debuggroup summary 1.46s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 2.00s debug will appear for these features: output,summary debuggroup summary 2.02s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-increased-circos.png debuggroup summary 2.02s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-increased-circos.svg debuggroup summary 2.05s parsing karyotype and organizing ideograms debuggroup summary 2.05s karyotype has 1 chromosomes of total size 101 debuggroup summary 2.05s applying global and local scaling debuggroup summary 2.05s allocating image, colors and brushes debuggroup summary 5.50s drawing 1 ideograms of total size 101 debuggroup summary 5.50s drawing highlights and ideograms debuggroup summary 5.50s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 5.51s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local//genes.formatted.txt debuggroup summary 5.61s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 5.61s process track_0 link /tmp/6963270.1.websrv1.q/tmp2emwu1ed//data/circos.bplinks.txt debuggroup summary 5.83s drawing link track_0 z 50 debuggroup output 6.38s generating output debuggroup output 6.92s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-increased-circos.png (184 kb) debuggroup output 7.02s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/local/RNA-MUTANT-increased-circos.svg (92 kb) =============================== $(which remuRNA) /tmp/6963270.1.websrv1.q/tmpt8nzwgwf.fa -p=1 ['SNP', 'H(wt||mu)', 'MFE(mu)', 'MFE(wt)', 'dMFE'] -m 1 ERROR: RNASNP returned warning for: /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/input_rna.fa message is:Warnings: The input sequence length 100 is less than twice the size of chosen flanking size 200. Thus, the reporting p-value is not accurate. Please refer to the README file for more details. SNP w Slen GC interval d_max p-value interval r_min p-value G19U 200 100 0.6200 12-78 0.2105 0.0952 18-67 0.4783 0.2191 ['SNP', 'interval', 'd_max', 'p-value'] -m 2 ERROR: RNASNP returned warning for: /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/input_rna.fa message is:Warnings: The input sequence length 100 is less than twice the size of chosen flanking size 200. Thus, the reporting p-value is not accurate. Please refer to the README file for more details. SNP w Slen GC max_k d_max p-value interval d p-value G19U 200 100 0.6200 8 13.3894 0.0121 8-89 0.2083 0.0421 ['SNP', 'interval', 'd', 'p-value'] SNP scores were saved to: /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/remuRNA.csv /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_7212798/RNAsnp.csv