Visualization fails without much error information

[aldendirks]

Thanks for your great tool! It worked for me up to the last step. When I attempt to run circos I get this error:

error: could not execute circos on commandline for FUNA, exiting..
Inappropriate ioctl for device

The previous output and alignments produced by MAFFT do seem to show a starship insertion (tyr captain present, DR and TIR present). There isn't more information so I'm not sure what is failing with circos.

[aldendirks]

When I run the command in the tutorial (with or without the flanking file)

starfish pair-viz -m all -t empty -T 2 -A nucmer -a $out/combined/assemblies.txt -b $out/combined/elementFinder/genbank.elements.bed -S $out/combined/elementFinder/genbank.elements.named.stats -o $out/combined/pairViz/ -f $out/combined/elementFinder/genbank.flank.singleDR.stats

I get this output:

[Thu Jul 10 19:48:29 2025] executing command: starfish pair-viz -m all -t empty -T 2 -A nucmer -a /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/starfish/combined/assemblies.txt -b /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/starfish/combined/elementFinder/genbank.elements.bed -S /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/starfish/combined/elementFinder/genbank.elements.named.stats -o /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/starfish/combined/pairViz/ -f /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/starfish/combined/elementFinder/genbank.flank.singleDR.stats

Warning: multi-threading currently not supported for --aligner nucmer
Key parameters:
--upstream             100000
--downstream           100000
nucmer                 --mum
delta-filter           -m -l 1000 -i 90

[Thu Jul 10 19:48:29 2025] reading in data..
[Thu Jul 10 19:49:12 2025] parsing comparisons..
[Thu Jul 10 19:49:12 2025] executing nucmer alignments..
[Thu Jul 10 19:49:25 2025] executing circos..


[Thu Jul 10 19:49:25 2025] warning: could not execute circos on commandline for GENPX_s00011 and Q9L49_scaffold-6, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:26 2025] warning: could not execute circos on commandline for GENGV_s00005 and Q9L65_scaffold-49, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:28 2025] warning: could not execute circos on commandline for GENPX_s00009 and Q9L49_scaffold-3, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:29 2025] warning: could not execute circos on commandline for Q9L58_s00033 and Q9L83_scaffold-324, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:30 2025] warning: could not execute circos on commandline for Q9M06_s00123 and Q9M05_scaffold-661, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:31 2025] warning: could not execute circos on commandline for Q9L49_s00016 and GENPX_scaffold-1, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:32 2025] warning: could not execute circos on commandline for GENGV_s00006 and Q9M04_scaffold-10, skipping..
Inappropriate ioctl for device


[Thu Jul 10 19:49:33 2025] warning: could not execute circos on commandline for FUNA_s00002 and Q9L68_scaffold-91, skipping..
Inappropriate ioctl for device
[Thu Jul 10 19:49:34 2025] done

When I change it to -A mafft, I only get the mafft aligments as output, nothing else and no errors.

[egluckthaler]

hmm what machine are you using? can you verify that you can run circos in the starfish conda environment perhaps using some of the circos test data? can you also confirm that nucmer generated the correct alignment files?