CIRCOS ERROR cmd: circos -noparanoid -conf test.conf

[ykkim0127]

I got this circos error when I run Jupiter using own test data using Ecoli. All perl modules are downloaded and I am stuck in this step.. How can I solve this ? I editted pathway information, because it looks messy to read.

-- bash 1_jupiter_script.sh grep -v XA test-agp.sam | grep -v '^@' | awk '{if($5 > 50 || $5 == "" ) print}' | perl JupiterPlot-1.0/bin/samToBed.pl > test-agp.bed samtools faidx test_scaffolds.fa perl JupiterPlot-1.0/bin/generateConf.pl -n 75 -r JupiterPlot-1.0/config/rawConf.conf -p test -s test_scaffolds.fa.fai -b test-agp.bed -a test.agp -k test_reference.karyotype sed: -e expression #1, char 18: unknown option to s' sed: -e expression #1, char 14: unknown option tos' Generating Karyotype file Selecting 2 scaffolds to render Generating Links file chromosomes_order = scaf1,ref0 cat test.rv.links | JupiterPlot-1.0/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks -max_gap 100000 -min_bundle_size 10000 > test.rv.links.bundled num_links 27 num_initial_bundles 15 num_links_in_initial_bundles 27 num_passed_bundles 0 (0.00%) num_links_in_passed_bundles 0 (0.00%) cat test.fw.links | JupiterPlot-1.0/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks -max_gap 100000 -min_bundle_size 10000 > test.fw.links.bundled num_links 265 num_initial_bundles 9 num_links_in_initial_bundles 265 num_passed_bundles 1 (11.11%) num_links_in_passed_bundles 247 (93.21%) 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 perl JupiterPlot-1.0/circos-0.69-3/bin/circos -noparanoid -conf test.conf debuggroup summary 0.16s welcome to circos v0.69-3 24 Jun 2016 on Perl 5.026001 debuggroup summary 0.16s current working directory circos-test debuggroup summary 0.16s command JupiterPlot-1.0/circos-0.69-3/bin/circos -noparanoid -conf test.conf debuggroup summary 0.16s loading configuration from file test.conf debuggroup summary 0.16s found conf file test.conf debuggroup summary 0.28s debug will appear for these features: output,summary

CIRCOS ERROR

  cwd: circos-test

  command: JupiterPlot-1.0/circos-0.69-3/bin/circos
  -noparanoid -conf test.conf

Cannot find the directory [./circos-test] for writing image files.

If you are having trouble debugging this error, first read the best practices tutorial for helpful tips that address many common problems

  http://www.circos.ca/documentation/tutorials/reference/best_practices

The debugging facility is helpful to figure out what's happening under the hood

  http://www.circos.ca/documentation/tutorials/configuration/debugging

If you're still stumped, get support in the Circos Google Group. Please include this error and all your configuration and data files.

  http://groups.google.com/group/circos-data-visualization

Stack trace: at JupiterPlot-1.0/circos-0.69-3/bin/../lib/Circos/Error.pm line 423. Circos::Error::fatal_error("io", "no_directory", ".circos-test", "image files") called at circos-0.69-3/bin/../lib/Circos.pm line 167 Circos::run("Circos", "_argv", "-noparanoid -conf circos-test"..., "paranoid", 0, "_cwd", "circos-test", "configfile", ...) called at JupiterPlot-1.0/circos-0.69-3/bin/circos line 529 JupiterPlot-1.0/jupiter:100: recipe for target 'circos-test/test.svg' failed make: *** [circos-test/test.svg] Error 255 rm test.links.final circos-test/test.rv.links.bundled test-agp.bed est.conf test.fw.links.bundled test_scaffolds.fa.fai test.fw.links.bundled.flipped

--

And as a result of running Jupiter, I got those outputs. Apr 4 02:30 1_jupiter_script.sh 4.0K Apr 4 02:22 Ecoli-K12 drw4.0K Apr 4 02:23 Ecoli-O157 188 Apr 4 02:30 test.agp 5.4M Apr 4 02:30 test-agp.fa 16M Apr 4 02:30 test-agp.sam 16K Apr 4 11:40 test.fw.links 69 Apr 4 11:40 test.karyotype 124 Apr 4 02:30 test_reference.fa -> GCF_000005845.2_ASM584v2_genomic.fna 12 Apr 4 02:30 test_reference.fa.amb 39 Apr 4 02:30 test_reference.fa.ann 1.2M Apr 4 02:30 test_reference.fa.pac 2.3M Apr 4 02:30 test_reference.fa.sa 33 Apr 4 02:30 test_reference.karyotype 1.6K Apr 4 11:40 test.rv.links 125 Apr 4 02:30 test_scaffolds.fa -> GCF_000008865.2_ASM886v2_genomic.fna 30 Apr 4 11:40 test.seqOrder.txt

[JustinChu]

What is in your 1_jupiter_script.sh ? Also what OS are you running?

[JustinChu]

There also does appear to be something odd happening in the sed command in one of the scripts. Can you also run sed --version in your console?

[ykkim0127]

Hi. Thanks for promt reply.

Ths script is as below,

jupiter name=./circos-test/test ref=GCF_000005845.2_ASM584v2_genomic.fna fa=GCF_000008865.2_ASM886v2_genomic.fna t=96

And when I run sed --version, it prints

sed (GNU sed) 4.4
Copyright (C) 2017 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Jay Fenlason, Tom Lord, Ken Pizzini,
and Paolo Bonzini.
GNU sed home page: <http://www.gnu.org/software/sed/>.
General help using GNU software: <http://www.gnu.org/gethelp/>.
E-mail bug reports to: <bug-sed@gnu.org>.

[JustinChu]

Hmm I think the syntax issues originate using a name that I did not expect. I that is didn't expect people to output the file to another directory. Try to run it with a name without any /.

[ykkim0127]

Without path information, error is fixed ! Thanks for quick help.