Download an archive file containing the complete results produced by the job in
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Results file content
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