search

luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
301 stars 37 forks source link

Discover_tz_dir failed to find zoneinfo #149

Closed jbedo closed 3 years ago

jbedo commented 3 years ago

Describe the bug

The latest release of Octopus (0.7.1) now triggers the error

[2021-03-07 21:59:48] <INFO> ------------------------------------------------------------------------
[2021-03-07 21:59:48] <INFO> octopus v0.7.1
[2021-03-07 21:59:48] <INFO> Copyright (c) 2015-2020 University of Oxford
[2021-03-07 21:59:48] <INFO> ------------------------------------------------------------------------
[2021-03-07 21:59:48] <WARN> The population calling model is still in development. Do not use for production work!
[2021-03-07 21:59:48] <INFO> Done initialising calling components in 131ms
[2021-03-07 21:59:48] <INFO> Detected 2 samples: "mysample1" "mysample2"
[2021-03-07 21:59:48] <INFO> Invoked calling model: population
[2021-03-07 21:59:48] <INFO> Processing 59,880bp with 24 threads (24 cores detected)
[2021-03-07 21:59:48] <INFO> Writing filtered calls to "/nix/store/f19m8qqd9c9x8s3x4b5nzbii2abvj8wj-bionix-octopus-call"
[2021-03-07 21:59:48] <EROR> An unclassified error has occurred:
[2021-03-07 21:59:48] <EROR>
[2021-03-07 21:59:48] <EROR>     Discover_tz_dir failed to find zoneinfo
.
[2021-03-07 21:59:48] <EROR>
[2021-03-07 21:59:48] <EROR> To help resolve this error submit an error report.
[2021-03-07 21:59:48] <INFO> ------------------------------------------------------------------------

Version

octopus version 0.7.1
Target: x86_64 Linux 5.4.67
SIMD extension: SSE2
Compiler: GNU 10.2.0
Boost: 1_69

Command line to run octopus:

$ octopus -R ref.fa -I *.bam -o $out \
  --bamout $evidence \
  --threads=$NIX_BUILD_CORES \
dancooke commented 3 years ago

Thanks. Please re-open if 3dbd8cc33616129ad356e99a4dae82e4f6702250 doesn't resolve the issue.

jbedo commented 3 years ago

Problem remains, exact same error with the patch:

[2021-03-08 21:23:27] <INFO> ------------------------------------------------------------------------
[2021-03-08 21:23:27] <INFO> octopus v0.7.1
[2021-03-08 21:23:27] <INFO> Copyright (c) 2015-2020 University of Oxford
[2021-03-08 21:23:27] <INFO> ------------------------------------------------------------------------
[2021-03-08 21:23:27] <WARN> The population calling model is still in development. Do not use for production work!
[2021-03-08 21:23:27] <INFO> Done initialising calling components in 154ms
[2021-03-08 21:23:27] <INFO> Detected 2 samples: "mysample1" "mysample2"
[2021-03-08 21:23:27] <INFO> Invoked calling model: population
[2021-03-08 21:23:27] <INFO> Processing 59,880bp with 24 threads (24 cores detected)
[2021-03-08 21:23:27] <INFO> Writing filtered calls to "/nix/store/gq1j3w07rvgan5msf5qragg6i5xrnidg-bionix-octopus-call"
[2021-03-08 21:23:27] <EROR> An unclassified error has occurred:
[2021-03-08 21:23:27] <EROR> 
[2021-03-08 21:23:27] <EROR>     Discover_tz_dir failed to find zoneinfo
.
[2021-03-08 21:23:27] <EROR> 
[2021-03-08 21:23:27] <EROR> To help resolve this error submit an error report.
[2021-03-08 21:23:27] <INFO> ------------------------------------------------------------------------
dancooke commented 3 years ago

Are you using the Docker image at dancooke/octopus:latest?

jbedo commented 3 years ago

No, I'm updating the octopus expression in nixpkgs to the latest release (I'm the package maintainer). Octopus build fine but fails to execute in our sandbox. TZ info isn't available in our sandbox for reproducibility reasons.

dancooke commented 3 years ago

Please can you try af5a66a2792bd098fb53eb79fb4822625f09305e?

jbedo commented 3 years ago

Issue resolved, thanks!

jbedo commented 3 years ago

This seems to still be an issue in the latest release (0.7.3). The two commits still resolve it when backported.

dancooke commented 3 years ago

Oh bugger! Looks like I accidentally reverted those commits along with the cancer model fixes when packaging the previous release. I've just un-reverted them on develop. I'll probably package them into a new release later today.

jbedo commented 3 years ago

Thanks! I was quite confused by that :D.