search

luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
302 stars 38 forks source link

Failed to download forest germline.v0.7.0.forest.gz #124

Closed satzel closed 4 years ago

satzel commented 4 years ago

Describe the bug Hiya, I tried to install the option to run filtering using random forest but can't download germline.v0.7.0.forest.gz or somatic.v0.7.0.forest.gz When checking the google bucket only version 0.6.0. and 0.6.3 seem to be there

Version

$ octopus --version
// PASTE OUTPUT HERE

octopus version 0.7.0 (develop 595f8917) Target: x86_64 Linux 3.10.0-957.10.1.el7.x86_64 SIMD extension: AVX512 Compiler: GNU 9.2.0 Boost: 1_72

Command Command line to install octopus:

$ ./scripts/install.py --forests --htslib /apps/eb/skylake/software/HTSlib/1.9-foss-2018b
dancooke commented 4 years ago

Hey, unfortunately the v0.7.0 forests are not available just yet - I'll make them available once v0.7.0 is a tagged release. Note that the earlier forest versions won't work with the latest develop build of Octopus, so your options are either to just use. v0.6.3b, or train your own forest.

dancooke commented 4 years ago

Duplicate of #103.

satzel commented 4 years ago

is it easy enough to down grade to v0.6.3b? I can search myself, unless there is a super quick pointer you can post? thanks alot :)

dancooke commented 4 years ago

You can either checkout release/v0.6.3-beta, or download the tarball here, or install via Bioconda.

satzel commented 4 years ago

Ok I got octopus v0.6.3-beta (release/0.6.3-beta 8b0e2968) and downloaded the two respective forest files from the goolgle bucket and when I run this command:

/octopus.v.6.3/octopus/bin/octopus -R ref/Homo_sapiens_assembly38.fasta -I blood_01_recal.bam\ -C cancer \ --forest /octopus.v.6.3/octopus/resources/forests/germline.v0.6.3-beta.forest \ --somatic-forest /octopus.v.6.3/octopus/resources/forests/somatic.v0.6.3-beta.forest\ --debug \ -o filtered.octopus_both.vcf.gz

I get: 2020-05-21 09:07:04] Encountered an error whilst calling, attempting to cleanup [2020-05-21 09:07:04] Removed 2 temporary files [2020-05-21 09:07:04] - 100% 9m 4s - [2020-05-21 09:07:04] A program error has occurred: [2020-05-21 09:07:04] [2020-05-21 09:07:04] Encountered an exception during calling 'std::bad_alloc'. This means [2020-05-21 09:07:04] there is a bug and your results are untrustworthy. [2020-05-21 09:07:04] [2020-05-21 09:07:04] To help resolve this error run in debug mode and send the log file to [2020-05-21 09:07:04] https://github.com/luntergroup/octopus/issues. [2020-05-21 09:07:04] ------------------------------------------------------------------------

I ran in debug mode and got the log file but its 70MB, shall I uplaod it here?

I could run variant calling in cancer mode on the same file in v0.7.0 without errors but then I couldn't add the forests.

Do you have advise for this? Many thanks :)

--version octopus version 0.6.3-beta (release/0.6.3-beta 8b0e2968) Target: x86_64 Linux 3.10.0-957.10.1.el7.x86_64 Compiler: GNU 7.3.0 Boost: 1_67

dancooke commented 4 years ago

Likely that this is a bug in v0.6.3b that's been fixed in v0.7.0. Unfortunately, you'll need to wait until v0.7.0 is released to access the new forests. Shouldn't be too much longer now!