circos plotting error

[mjmillerlab]

Trying out this software. Really excited for a circos plot. However, it seems to fail in the drawing stage. This is the last bit of code (there is more of these "Use of..." above):

Use of uninitialized value $chromosomes{"ref61"} in concatenation (.) or string at /home/mmiller/JupiterPlot-master/bin/generateConf.pl line 388, line 4338. has no alignments Use of uninitialized value $chromosomes{"ref63"} in concatenation (.) or string at /home/mmiller/JupiterPlot-master/bin/generateConf.pl line 388, line 4338. has no alignments anna_chromW has no alignments Use of uninitialized value $chromosomes{"ref65"} in concatenation (.) or string at /home/mmiller/JupiterPlot-master/bin/generateConf.pl line 388, line 4338. has no alignments anna_chromZ_RaGOO has no alignments cat test.rv.links | /home/mmiller/JupiterPlot-master/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks -max_gap 100000 -min_bundle_size 50000 > test.rv.links.bundled num_links 112 num_initial_bundles 38 num_links_in_initial_bundles 112 num_passed_bundles 0 (0.00%) num_links_in_passed_bundles 0 (0.00%)

cat test.rv.links | perl /home/mmiller/JupiterPlot-master/bin/linkCollapse.pl -m 100000 -b 50000 > test.rv.links.bundled #simple bundle

cat test.fw.links | /home/mmiller/JupiterPlot-master/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks -max_gap 100000 -min_bundle_size 50000 > test.fw.links.bundled num_links 1020 num_initial_bundles 147 num_links_in_initial_bundles 1020 num_passed_bundles 5 (3.40%) num_links_in_passed_bundles 615 (60.29%)

cat test.fw.links | perl /home/mmiller/JupiterPlot-master/bin/linkCollapse.pl -m 100000 -b 50000 > test.fw.links.bundled #simple bundle

awk ' { t = $5; $5 = $6; $6 = t; print; } ' test.fw.links.bundled > test.fw.links.bundled.flipped cat test.rv.links.bundled test.fw.links.bundled.flipped > test.links.final circos -noparanoid -conf test.conf debuggroup summary 0.19s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002 debuggroup summary 0.19s current working directory /home/mmiller/JupiterPlot-master debuggroup summary 0.19s command /home/mmiller/miniconda3/bin/circos -noparanoid -conf test.conf debuggroup summary 0.19s loading configuration from file test.conf debuggroup summary 0.19s found conf file test.conf debuggroup summary 0.35s debug will appear for these features: output,summary debuggroup summary 0.35s bitmap output image ./test.png debuggroup summary 0.35s SVG output image ./test.svg debuggroup summary 0.35s parsing karyotype and organizing ideograms Use of uninitialized value $start in substitution (s///) at /home/mmiller/miniconda3/bin/../lib/Circos/Karyotype.pm line 128, line 2. Use of uninitialized value $end in substitution (s///) at /home/mmiller/miniconda3/bin/../lib/Circos/Karyotype.pm line 129, line 2.

CIRCOS ERROR

  cwd: /home/mmiller/JupiterPlot-master

  command: /home/mmiller/miniconda3/bin/circos -noparanoid -conf test.conf

Start [undef] and/or end [undef] coordinate in karyotype file don't appear to be numbers. Thousands separators , and _ are allowed, but not any other characters.

[JustinChu]

That is an odd error. Can you post the first few line of the following files:

test.links.final
test.karyotype

Also what is the first error you see when the script generateConf.pl runs to generate the test.conf file?

There could also be issues related to the naming convention of your input reference file or scaffolds or possibly extra newlines in those files that some scripts didn't account for in the code.

[drashwinelkar]

I think I reposted the same issue as a new one. You could check. I get the exact same error. I am changing how my scaffolds are named to check if it resolves the problem.

[drashwinelkar]

I changed the way the sequences are named but the error still persists.

[JustinChu]

Likely fixed in #27