cd /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/; RNAplfold -W 200 -L 150 -u 9 < /tmp/6963248.1.websrv1.q/tmpg16chxh5 b'' b'' snp_locs: [] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/' --prefix 'RNA-WILDTYPE-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA_dp.ps' --title 'RNA-WILDTYPE' tmpdir is: /tmp/6963248.1.websrv1.q/tmpfecflzjy/ ['/tmp/6963248.1.websrv1.q/tmpfecflzjy/data/sequence.txt', '/tmp/6963248.1.websrv1.q/tmpfecflzjy/data/circos.sequence.txt', '/tmp/6963248.1.websrv1.q/tmpfecflzjy/data/circos.karyotype.txt', '/tmp/6963248.1.websrv1.q/tmpfecflzjy/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**="RNA-WILDTYPE-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmpfecflzjy//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmpfecflzjy//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 3.38s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 3.42s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 3.42s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**=RNA-WILDTYPE-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmpfecflzjy//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmpfecflzjy//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 3.42s guessing configuration file debuggroup summary 3.46s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 6.50s debug will appear for these features: output,summary debuggroup summary 6.52s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-WILDTYPE-circos.png debuggroup summary 6.52s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-WILDTYPE-circos.svg debuggroup summary 6.60s parsing karyotype and organizing ideograms debuggroup summary 6.60s karyotype has 1 chromosomes of total size 202 debuggroup summary 6.60s applying global and local scaling debuggroup summary 6.60s allocating image, colors and brushes debuggroup summary 23.69s drawing 1 ideograms of total size 202 debuggroup summary 23.69s drawing highlights and ideograms debuggroup summary 23.76s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 23.87s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt debuggroup summary 24.09s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 24.13s process track_0 link /tmp/6963248.1.websrv1.q/tmpfecflzjy//data/circos.bplinks.txt debuggroup summary 24.72s drawing link track_0 z 50 debuggroup output 25.93s generating output debuggroup output 26.61s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-WILDTYPE-circos.png (291 kb) debuggroup output 26.78s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-WILDTYPE-circos.svg (246 kb) =============================== cd /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/; RNAplfold -W 200 -L 150 -u 9 < /tmp/6963248.1.websrv1.q/tmpge2uacky b'' b'' snp_locs: [101] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/' --prefix 'RNA-MUTANT-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT_dp.ps' --title 'RNA-MUTANT' tmpdir is: /tmp/6963248.1.websrv1.q/tmp36q98xlr/ ['/tmp/6963248.1.websrv1.q/tmp36q98xlr/data/sequence.txt', '/tmp/6963248.1.websrv1.q/tmp36q98xlr/data/circos.sequence.txt', '/tmp/6963248.1.websrv1.q/tmp36q98xlr/data/circos.karyotype.txt', '/tmp/6963248.1.websrv1.q/tmp36q98xlr/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**="RNA-MUTANT-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmp36q98xlr//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmp36q98xlr//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 1.37s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 1.41s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 1.41s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**=RNA-MUTANT-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmp36q98xlr//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmp36q98xlr//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 1.41s guessing configuration file debuggroup summary 1.41s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 2.22s debug will appear for these features: output,summary debuggroup summary 2.22s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-circos.png debuggroup summary 2.22s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-circos.svg debuggroup summary 2.27s parsing karyotype and organizing ideograms debuggroup summary 2.28s karyotype has 1 chromosomes of total size 202 debuggroup summary 2.28s applying global and local scaling debuggroup summary 2.28s allocating image, colors and brushes debuggroup summary 5.86s drawing 1 ideograms of total size 202 debuggroup summary 5.86s drawing highlights and ideograms debuggroup summary 5.86s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 5.89s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt debuggroup summary 6.02s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 6.03s process track_0 link /tmp/6963248.1.websrv1.q/tmp36q98xlr//data/circos.bplinks.txt debuggroup summary 6.62s drawing link track_0 z 50 debuggroup output 7.81s generating output debuggroup output 8.62s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-circos.png (278 kb) debuggroup output 8.87s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-circos.svg (240 kb) =============================== min_max is [81, 140] cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/' --prefix 'RNA-MUTANT-weakened-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT_dp_diff_weakened.dp' --title 'RNA-MUTANT-weakened' tmpdir is: /tmp/6963248.1.websrv1.q/tmpj_79t54v/ ['/tmp/6963248.1.websrv1.q/tmpj_79t54v/data/sequence.txt', '/tmp/6963248.1.websrv1.q/tmpj_79t54v/data/circos.sequence.txt', '/tmp/6963248.1.websrv1.q/tmpj_79t54v/data/circos.karyotype.txt', '/tmp/6963248.1.websrv1.q/tmpj_79t54v/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**="RNA-MUTANT-weakened-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmpj_79t54v//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmpj_79t54v//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 1.32s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 1.36s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 1.36s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**=RNA-MUTANT-weakened-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmpj_79t54v//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmpj_79t54v//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 1.36s guessing configuration file debuggroup summary 1.36s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 1.98s debug will appear for these features: output,summary debuggroup summary 1.98s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-weakened-circos.png debuggroup summary 1.98s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-weakened-circos.svg debuggroup summary 2.01s parsing karyotype and organizing ideograms debuggroup summary 2.02s karyotype has 1 chromosomes of total size 202 debuggroup summary 2.02s applying global and local scaling debuggroup summary 2.02s allocating image, colors and brushes debuggroup summary 5.64s drawing 1 ideograms of total size 202 debuggroup summary 5.64s drawing highlights and ideograms debuggroup summary 5.64s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 5.68s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt debuggroup summary 5.82s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 5.83s process track_0 link /tmp/6963248.1.websrv1.q/tmpj_79t54v//data/circos.bplinks.txt debuggroup summary 6.04s drawing link track_0 z 50 debuggroup output 6.46s generating output debuggroup output 7.11s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-weakened-circos.png (180 kb) debuggroup output 7.25s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-weakened-circos.svg (90 kb) =============================== cd "/scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/"; python dot2circ.py --outputdir '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/' --prefix 'RNA-MUTANT-increased-circos' --dp-file '/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT_dp_diff_increased.dp' --title 'RNA-MUTANT-increased' tmpdir is: /tmp/6963248.1.websrv1.q/tmp8aq5n3_h/ ['/tmp/6963248.1.websrv1.q/tmp8aq5n3_h/data/sequence.txt', '/tmp/6963248.1.websrv1.q/tmp8aq5n3_h/data/circos.sequence.txt', '/tmp/6963248.1.websrv1.q/tmp8aq5n3_h/data/circos.karyotype.txt', '/tmp/6963248.1.websrv1.q/tmp8aq5n3_h/data/circos.bplinks.txt'] calling: " circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**="RNA-MUTANT-increased-circos.png" -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmp8aq5n3_h//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmp8aq5n3_h//data/circos.bplinks.txt -param ideogram/show_label=yes " ======circos output log======== debuggroup summary 2.43s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 2.47s current working directory /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ debuggroup summary 2.47s command /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/circos -outputdir /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/ -param image/file**=RNA-MUTANT-increased-circos.png -param image/radius*=1000p -param karyotype=/tmp/6963248.1.websrv1.q/tmp8aq5n3_h//data/circos.karyotype.txt -param highlights/highlight/file=/scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt -param links/link/file=/tmp/6963248.1.websrv1.q/tmp8aq5n3_h//data/circos.bplinks.txt -param ideogram/show_label=yes debuggroup summary 2.47s guessing configuration file debuggroup summary 2.47s found conf file /scratch/rna/bisge001/Software/MutaRNA/1.3/bin/dot2circ/circos.conf debuggroup summary 3.70s debug will appear for these features: output,summary debuggroup summary 3.71s bitmap output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-increased-circos.png debuggroup summary 3.71s SVG output image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-increased-circos.svg debuggroup summary 3.78s parsing karyotype and organizing ideograms debuggroup summary 3.78s karyotype has 1 chromosomes of total size 202 debuggroup summary 3.78s applying global and local scaling debuggroup summary 3.78s allocating image, colors and brushes debuggroup summary 7.84s drawing 1 ideograms of total size 202 debuggroup summary 7.84s drawing highlights and ideograms debuggroup summary 7.84s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/highlight.bg.conf debuggroup summary 7.88s process track_0 highlight /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local//genes.formatted.txt debuggroup summary 8.01s found conf file /scratch/rna/bisge001/Software/conda-v4.6.0/envs/MutARNA-1.0/bin/../etc/tracks/link.conf debuggroup summary 8.03s process track_0 link /tmp/6963248.1.websrv1.q/tmp8aq5n3_h//data/circos.bplinks.txt debuggroup summary 8.25s drawing link track_0 z 50 debuggroup output 8.71s generating output debuggroup output 9.40s created PNG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-increased-circos.png (193 kb) debuggroup output 9.53s created SVG image /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/local/RNA-MUTANT-increased-circos.svg (96 kb) =============================== $(which remuRNA) /tmp/6963248.1.websrv1.q/tmpamokriwa.fa -p=1 ['SNP', 'H(wt||mu)', 'MFE(mu)', 'MFE(wt)', 'dMFE'] -m 1 SNP w Slen GC interval d_max p-value interval r_min p-value A101C 200 201 0.3383 86-139 0.4163 0.0104 85-135 -0.1571 0.0417 ['SNP', 'interval', 'd_max', 'p-value'] -m 2 SNP w Slen GC max_k d_max p-value interval d p-value A101C 200 201 0.3383 96 17.9079 0.0028 96-139 0.4243 0.0020 ['SNP', 'interval', 'd', 'p-value'] SNP scores were saved to: /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/remuRNA.csv /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_9510481/RNAsnp.csv