Ensemble "Problem retrieving reference variant"

[golrokh51]

bcbio.variation.recall ensemble
version: 0.1.7
names=bcfsnp,vscan2snp,vscan2indl,mutec2
command: bcbio-variation-recall ensemble --cores 40 --numpass 1 --names $names $out $ref $snp $vsnp $vindl $mutec

my error:
2020-09-04 13:18:52 blg9325.int.ets1.calculquebec.ca ERROR [bcbio.variation.recall.main] - java.lang.Exception: Problem retrieving reference variant for {:chr "chr1", :start 100, :refa "T", :alta [ "."], :end 101, :vc-indices (0)}: []

Could you please help me with this error?

If the problem is the version, I can not install the newest version as I am working on an HPC and anaconda and Docker are not available on it.

[roryk]

Hi @golrokh51,

Does your reference file specified in $ref match up with the names listed in the top of your VCF file?

Your version is super duper old. You don't need root or anything to install anaconda, if you want to use the newest version, you can install it like this:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86.sh
bash Miniconda3-latest-Linux-x86.sh

and following the instructions. Then re-login and do:

conda install -c bioconda bcbio-variation-recall

which should get you up to date. 1.7 is from 5 years ago! Let me know if you have trouble getting the conda install to work, it should work anywhere and needs almost nothing installed on the server.

[golrokh51]

Hi, Thanks. Yes my reference file specified in $ref match up with the names listed in the VCF file? I know. I will contact the support group to see if it is possible to install the new version. The HPC I use does not allow anaconda. Thanks for your help. I will change the headers and try it again but anyway I should ask them to install the new version themselves if we can't install it due to Anaconda limitations. Thanks for your help. I might bother you again 😅 Golrokh

…

On Sat, Sep 5, 2020 at 8:39 AM Rory Kirchner ***@***.***> wrote: Hi @golrokh51 <https://github.com/golrokh51>, Does your reference file specified in $ref match up with the names listed in the top of your VCF file? Your version is super duper old. You don't need root or anything to install anaconda, if you want to use the newest version, you can install it like this: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86.sh bash Miniconda3-latest-Linux-x86.sh and following the instructions. Then re-login and do: conda install -c bioconda bcbio-variation-recall which should get you up to date. 1.7 is from 5 years ago! Let me know if you have trouble getting the conda install to work, it should work anywhere and needs almost nothing installed on the server. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5TQOJVSZGVHNM7DU2GMDSEIWRLANCNFSM4QZIGQCQ> .

-- Golrokh

[golrokh51]

Dear Rory, When I tried to install it using the bash script, I got this error: installing: python-3.7.1-h0371630_7 ... Miniconda3-latest-Linux-x86.sh: line 373: /home/golrokh/miniconda3/pkgs/python-3.7.1-h0371630_7/bin/python: No such file or directory However, this directory exists

…

On Sat, Sep 5, 2020 at 8:39 AM Rory Kirchner ***@***.***> wrote: Hi @golrokh51 <https://github.com/golrokh51>, Does your reference file specified in $ref match up with the names listed in the top of your VCF file? Your version is super duper old. You don't need root or anything to install anaconda, if you want to use the newest version, you can install it like this: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86.sh bash Miniconda3-latest-Linux-x86.sh and following the instructions. Then re-login and do: conda install -c bioconda bcbio-variation-recall which should get you up to date. 1.7 is from 5 years ago! Let me know if you have trouble getting the conda install to work, it should work anywhere and needs almost nothing installed on the server. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5TQOJVSZGVHNM7DU2GMDSEIWRLANCNFSM4QZIGQCQ> .

-- Golrokh

[roryk]

Hi @golrokh51,

Is this related to your HPC not allowing miniconda/anaconda/etc? I don't see how they would do that other than disabling the ability to run your own python and making you use theirs, are they doing that here?

[golrokh51]

Hi @roryk
I just tried to install it on another server with no limitation for conda, and still I get the same error:
installing: python-3.7.1-h0371630_7 ...
Miniconda3-latest-Linux-x86.sh: /bio-info/golrokh/miniconda3/pkgs/python-3.7.1-h0371630_7/bin/python: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory

The only similarity between two system is that both are CENTOS7.

[roryk]

Thanks, it looks like 32-bit libraries are missing from your system, does using the 64 bit installation work? https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

[golrokh51]

coolll it is working THANK @roryk