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