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umccr / umccrise

:snake: DRAGEN Tumor/Normal workflow post-processing
https://umccr.github.io/umccrise/
MIT License
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Paranoid circos error #111

Closed pdiakumis closed 10 months ago

pdiakumis commented 2 years ago

Randomly happens on both ICA and HPC, on multiple samples, not reproducibly, gets resolved after deleting circos colour cache file and restarting on HPC at least. Worth noting it only happens with the circos_baf rule. Need to figure out a different way to generate those it seems. Not high priority right now, but still annoying - 3 cases so far.

at /miniconda/envs/umccrise_hmf/bin/../lib/Circos/Error.pm line 425, <F> line 888.
    Circos::Error::fatal_error("warning", "paranoid") called at /miniconda/envs/umccrise_hmf/bin/../lib/Circos/Debug.pm line 396
    Circos::Debug::printwarning("Problem reading color cache file /tmp/circos.colorlist.trn.d3"...) called at /miniconda/envs/umccrise_hmf/bin/../lib/Circos/Colors.pm line 209
    Circos::Colors::allocate_colors(GD::Image=SCALAR(0x562bceb63e88)) called at /miniconda/envs/umccrise_hmf/bin/../lib/Circos.pm line 692
    Circos::run("Circos", "outputfile", "SBJ00987__MDX210224.circos_baf.png", "_cwd", "/scratch/working_dir/L2101016__L2101015", "outputdir", "work/SBJ00987__MDX210224/purple/circos_baf", "svg", ...) called at /miniconda/envs/umccrise_hmf/bin/circos line 536
pdiakumis commented 1 year ago

Closing since we haven't hit this in over a year.

pdiakumis commented 1 year ago

We just hit this coincidentally with a re-run of SBJ02091, added to the list above.

pdiakumis commented 1 year ago

And we got another one (umccr__cohort__umccrise__SBJ00743__L2100265__20231014ff91314a).

pdiakumis commented 1 year ago

I think we can actually add the -noparanoid option to the circos plot making:

-paranoid -noparanoid Make all warnings fatal or not (default: paranoid).
hongwingl commented 18 minutes ago

FYI, this error occurs because circos writes the color lists to a file in the tmp directory. When multiple circos runs at the same time, they could overwrite this file and cause issues. We are working on a fix.

This failure is a little difficult to reproduce, we might put in a speculative fix into purple by overriding the TMPDIR environment variable of CIRCOS