JustinChu
commented
4 years ago Install the Config::General module and you should be able to finish the pipeline. There are many issues here though beyond this message however.
The first is that it is concerning that the issue looks like we are reading in an empty karyotype file. Can you post what your karyotype files look like? It could be filtering based on the m parameter all the reference scaffolds out of the file. You can try setting m to 0. With regards to the lack of alignments it may be worth checking the input files as the alignments are performed independently of filtering.
drashwinelkar
I get this circos error when I run Jupiter. This error is to be found when I install circos via LinuxBrew or compile from source. So I guess it does not originate from circos itself.
circos -noparanoid -conf Ctet_ntJoin_k70_w1000.conf debuggroup summary 0.10s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026001 debuggroup summary 0.10s current working directory /home/ashwin/Projects/tetanus/trimmed_raw_data/ntJoin debuggroup summary 0.10s command /home/ashwin/sources/circos-0.69-9/bin/circos -noparanoid -conf Ctet_ntJoin_k70_w1000.conf debuggroup summary 0.10s loading configuration from file Ctet_ntJoin_k70_w1000.conf debuggroup summary 0.10s found conf file Ctet_ntJoin_k70_w1000.conf debuggroup summary 0.17s debug will appear for these features: output,summary debuggroup summary 0.17s bitmap output image ./Ctet_ntJoin_k70_w1000.png debuggroup summary 0.17s SVG output image ./Ctet_ntJoin_k70_w1000.svg debuggroup summary 0.17s parsing karyotype and organizing ideograms Use of uninitialized value $start in substitution (s///) at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos/Karyotype.pm line 128, line 2.
Use of uninitialized value $end in substitution (s///) at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos/Karyotype.pm line 129, line 2.
CIRCOS ERROR
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.
Stack trace: at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos/Error.pm line 425, line 2.
Circos::Error::fatal_error("data", "malformed_karyotype_coordinates", undef, undef) called at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos/Karyotype.pm line 131
Circos::Karyotype::read_karyotype_file("Ctet_ntJoin_k70_w1000.karyotype", HASH(0x564897bd1bf8)) called at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos/Karyotype.pm line 92
Circos::Karyotype::read_karyotype("file", "Ctet_ntJoin_k70_w1000.karyotype") called at /home/ashwin/sources/circos-0.69-9/bin/../lib/Circos.pm line 218
Circos::run("Circos", "_cwd", "/home/ashwin/Projects/tetanus/trimmed_raw_data/ntJoin", "_argv", "-noparanoid -conf Ctet_ntJoin_k70_w1000.conf", "paranoid", 0, "configfile", ...) called at /home/ashwin/sources/circos-0.69-9/bin/circos line 536
/home/ashwin/sources/JupiterPlot/jupiter:97: recipe for target 'Ctet_ntJoin_k70_w1000.svg' failed
make: [Ctet_ntJoin_k70_w1000.svg] Error 255
make: Deleting file 'Ctet_ntJoin_k70_w1000.svg'
rm Ctet_ntJoin_k70_w1000.links.final Ctet_ntJoin_k70_w1000.rv.links.bundled Ctet_ntJoin_k70_w1000.conf Ctet_ntJoin_k70_w1000.fw.links.bundled Ctet_ntJoin_k70_w1000_scaffolds.fa.fai Ctet_ntJoin_k70_w1000.fw.links.bundled.flipped
Any idea why this is happening or how to sort this out? Thanks!