circos killed in run

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Rexford Dumevi

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Apr 21, 2021, 2:48:26 PMApr 21
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Hi, i am running circos on the chromosomal data of E.coli and it keeps getting killed before the run is over. I will be glad if you can help me figure out whats happening.

The message from circos below:

debuggroup summary 0.23s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.030000
debuggroup summary 0.23s current working directory /home/rexford/Desktop/circos_chrom
debuggroup summary 0.23s command bin/circos-0.69-9/bin/circos --conf circos_plots/etc/circos.conf
debuggroup summary 0.23s loading configuration from file circos_plots/etc/circos.conf
debuggroup summary 0.23s found conf file circos_plots/etc/circos.conf
debuggroup summary 0.64s debug will appear for these features: output,summary
debuggroup summary 0.64s bitmap output image ./circos.png
debuggroup summary 0.64s SVG output image ./circos.svg
debuggroup summary 0.64s parsing karyotype and organizing ideograms
debuggroup summary 0.65s karyotype has 1 chromosomes of total size 5,273,098
debuggroup summary 0.65s applying global and local scaling
debuggroup summary 0.65s allocating image, colors and brushes
debuggroup summary 12.86s drawing 1 ideograms of total size 5,273,098
debuggroup summary 12.86s drawing highlights and ideograms
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.86s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/highlight.bg.conf
debuggroup summary 12.87s process track_0 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/background_highlights.txt
debuggroup summary 12.87s process track_1 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/gene_highlights.txt
debuggroup summary 13.89s process track_2 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/PS_highlights.txt
debuggroup summary 14.65s process track_3 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/TSS_highlights.txt
debuggroup summary 21.19s process track_4 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/sRNA_highlights.txt
debuggroup summary 21.55s process track_5 highlight /home/rexford/Desktop/circos_chrom/circos_plots/data/separators_highlights.txt
debuggroup summary 52.46s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/link.conf
debuggroup summary 52.47s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/link.conf
debuggroup summary 52.47s process track_0 link /home/rexford/Desktop/circos_chrom/circos_plots/data/regulatory_interactions.csv
debuggroup summary 52.47s process track_1 link /home/rexford/Desktop/circos_chrom/circos_plots/data/regulatory_interactions_2.csv
debuggroup summary 52.47s drawing link track_0 z 0
debuggroup summary 52.48s drawing link track_1 z 0
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.48s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.49s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.49s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.49s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.49s found conf file /home/rexford/Desktop/circos_chrom/bin/circos-0.69-9/bin/../etc/tracks/histogram.conf
debuggroup summary 52.49s processing track_0 histogram /home/rexford/Desktop/circos_chrom/circos_plots/data/LBO104_04minusTEX_forward.csv
debuggroup summary 259.18s processing track_1 histogram /home/rexford/Desktop/circos_chrom/circos_plots/data/LBO104_04plusTEX_forward.csv
debuggroup summary 499.71s processing track_2 histogram /home/rexford/Desktop/circos_chrom/circos_plots/data/LBO104_04minusTEX_reverse.csv
debuggroup summary 748.40s processing track_3 histogram /home/rexford/Desktop/circos_chrom/circos_plots/data/LBO104_04plusTEX_reverse.csv
Killed

Regards,
Thanks




Martin Krzywinski

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May 5, 2021, 5:20:08 PMMay 5
to circos-data-...@googlegroups.com
Email me all data/conf files.

Martin Krzywinski
science + art



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Rexford Dumevi

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May 6, 2021, 4:05:35 AMMay 6
to circos-data-...@googlegroups.com
Hello Martin,

FInd attached the data/conf files for your perusal.

Warm regards,





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REXFORD MAWUNYO DUMEVI,
University Hospital Münster (UKM)
Microbial Genome Plasticity group
Institute of Hygiene, Mendelstraße 7
48149 Münster
Germany
Email: Rexfordmaw...@ukmuenster.de 
contact: +49-15906446252
skype: rexford.dumevi1

www.ukmuenster.de




Rexford Dumevi

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May 21, 2021, 7:08:18 AMMay 21
to circos-data-...@googlegroups.com
Hello Martin,

This is a gentle reminder about my issue. Any update regarding the data I sent you?

warm regards,
Rexford 

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