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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Encountered an exception during calling 'std::bad_alloc' #163

Closed Fred-07 closed 3 years ago

Fred-07 commented 3 years ago

Hi, Octopus failed to complete the variant calling. Here are the last lines of the "debug log":

[2021-04-11 13:16:29] Writing completed task Y:27770551-27770724 that finished in 5ms [2021-04-11 13:16:29] - 100% 45m 27s - [2021-04-11 13:16:29] Merging 27 temporary VCF files [2021-04-11 13:16:31] Starting Call Set Refinement (CSR) filtering [2021-04-11 13:16:32] Encountered an error whilst filtering, attempting to cleanup [2021-04-11 13:16:32] Removed 56 temporary files [2021-04-11 13:16:32] A program error has occurred: [2021-04-11 13:16:32] [2021-04-11 13:16:32] Encountered an exception during calling 'std::bad_alloc'. This means [2021-04-11 13:16:32] there is a bug and your results are untrustworthy. [2021-04-11 13:16:32] [2021-04-11 13:16:32] To help resolve this error run in debug mode and send the log file to [2021-04-11 13:16:32] https://github.com/luntergroup/octopus/issues. [2021-04-11 13:16:32] ------------------------------------------------------------------------

complete log https://www.dropbox.com/s/e08mb9b7yt6hnoy/octopus_debug.log.gz?dl=0

Versions octopus v0.7.2 in singularity container singularity 3.2.0-1 Linux 3.10.0-862.el7.x86_64

dancooke commented 3 years ago

Thanks for the bug report. This appears to be an issue specific to the Docker/Singularity build as several other users have reported the same issue using a Singularity image. I'm wondering if this has something to do with how much memory is available to the container.

dancooke commented 3 years ago

The problem is that the forest file being used, octopus_forests_germline.v0.7.2.forest.gz, is gzipped - unfortunately the forest library used doesn't read gzipped files, so this needs to be decompressed before being given to Octopus. I'll leave this issue open to remind me to add some code checks for this.

Fred-07 commented 3 years ago

Thank you for the investigation. I am going to try again with uncompressed forest file.

brentp commented 2 years ago

Hi @dancooke is it possible to support compressed forest files? I'd like to include this in a docker image and the uncompressed size of 2.9GB is much harder to justify than the 367MB (for germline).

dancooke commented 2 years ago

@brentp Done (37e421ff8a0c57c560e154666c7a46d168761667). Note that, as mentioned in https://github.com/luntergroup/octopus/issues/211#issuecomment-940928823, the v0.7.4 forests aren't optimal for the HEAD develop branch version due to a change introduced in f110bb84f66d8754a65520a2595825748c73350c. I hope to have new forests released soon.

brentp commented 2 years ago

thanks very much! I'll watch for new forests.

tzvi909 commented 2 months ago

Hi, when will these new forests be available?