Error while running TBprofiler ver. 4.3.0

[ryobon-dev]

Hi, TBprofiler runs very well at one machine (ubuntsu using WSL), however, when I ran TBprofiler in the other machine (linux ubuntsu) I encountered the error as attached.

Could you find any issue on this ?

FY17N016.errlog.txt

[jodyphelan]

This seems to be the issue:

bcftools: symbol lookup error: /home/kansensho-linux/miniconda3/envs/TBprofiler2/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

Can you run bcftools just to see if that work ok? And also conda env export | grep bcftools to check the version?

[ryobon-dev]

Thanks for your quick response as usual.

Yes, I got the issue in below when I run bcftools.

(base) kansensho-linux@kansensholinux-X570-PG4:/media/d/iwamoto$ conda activate TBprofiler2 (TBprofiler2) kansensho-linux@kansensholinux-X570-PG4:/media/d/iwamoto$ bcftools bcftools: symbol lookup error: /home/kansensho-linux/miniconda3/envs/TBprofiler2/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

The version is shown in below. (TBprofiler2) kansensho-linux@kansensholinux-X570-PG4:/media/d/iwamoto$ conda env export | grep bcftools

• bcftools=1.12=h45bccc9_1 (TBprofiler2) kansensho-linux@kansensholinux-X570-PG4:/media/d/iwamoto$

Can you tell me how to fix the issue ?

[ryobon-dev]

As an additional information, my OS is Ubuntu 20.04.1 LTS.

Thanks,

[jodyphelan]

Could you try download this file and create the environment with it? tbp_v4.3.0_linux.txt

conda create --name TBprofiler2 --file tbp_v4.3.0_linux.txt

[ryobon-dev]

It is fine now. Thanks,

One small question. Does the mutation list implemented in TBprofiler for resistance prediction contain WHO catalogue or simply TBprofiler original list ?

[jodyphelan]

The default list contains a combination of the WHO catalogue and the original tb-profiler list. There is also another branch containing only the WHO catalogue available at https://github.com/jodyphelan/tbdb/blob/who/tbdb.csv.

[ryobon-dev]

Thanks,

It is great !

[ksw9]

Hi, Thanks @jodyphelan for your documentation of this. I ran into the same problem with bcftools but it was fixed using the conda env file you posted above. Just FYI: I do get some error messages when installing via conda :

SafetyError: The package for tb-profiler located at /home/kwalter/.conda/pkgs/tb-profiler-4.3.0-pypyh5e36f6f_0
appears to be corrupted. The path 'share/tbprofiler/tbdb.barcode.bed'
has an incorrect size.
  reported size: 74764 bytes
  actual size: 78600 bytes

SafetyError: The package for tb-profiler located at /home/kwalter/.conda/pkgs/tb-profiler-4.3.0-pypyh5e36f6f_0
appears to be corrupted. The path 'share/tbprofiler/tbdb.bed'
has an incorrect size.
  reported size: 2378 bytes
  actual size: 3448 bytes
...

Just wanted to let you know. Thank you again for your work on this! Best,

[jodyphelan]

Hi @ksw9 ,

Thanks for the feedback! I'm not sure what is going on with the conda install but I think it has something to do with one of the many dependencies clashing with existing installed software. Glad the env file worked for you. I'll try see if I can resolve the issue so that a normal install will work too.

I think the error messages are related to the bed files having been updated at some point on your system and not matching with the ones in the conda package. If you run update_tbdb this will happen for example. I think you can ignore them but let me know if you get any strange errors while running.

[ksw9]

Hi Jody, Yes, I think that’s it—I used the tb-profiler update_tbdb --match_ref command to update the chromosome name in my local tbdb.

Thanks!

From: Jody Phelan @.> Date: Thursday, September 29, 2022 at 5:50 PM To: jodyphelan/TBProfiler @.> Cc: Katharine Walter @.>, Mention @.> Subject: Re: [jodyphelan/TBProfiler] Error while running TBprofiler ver. 4.3.0 (Issue #236)

Hi @ksw9https://github.com/ksw9 ,

Thanks for the feedback! I'm not sure what is going on with the conda install but I think it has something to do with one of the many dependencies clashing with existing installed software. Glad the env file worked for you. I'll try see if I can resolve the issue so that a normal install will work too.

I think the error messages are related to the bed files having been updated at some point on your system and not matching with the ones in the conda package. If you run update_tbdb this will happen for example. I think you can ignore them but let me know if you get any strange errors while running.

— Reply to this email directly, view it on GitHubhttps://github.com/jodyphelan/TBProfiler/issues/236#issuecomment-1262944260, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABYOQ72RU7I27DNBK4DRHBLWAYTL5ANCNFSM6AAAAAAQILC354. You are receiving this because you were mentioned.Message ID: @.***>

[Mxrcon]

Hey @jodyphelan, I Just came across the same issue when v4.4.0 from a fresh installation from bioconda, perhaps modifying the file provided here > https://github.com/jodyphelan/TBProfiler/issues/236#issuecomment-1243853924 seems to fix the error.

-https://conda.anaconda.org/bioconda/noarch/tb-profiler-4.3.0-pypyh5e36f6f_0.tar.bz2
+https://conda.anaconda.org/bioconda/noarch/tb-profiler-4.4.0-pyh7cba7a3_0.tar.bz2

and then conda install quickle filelock did the trick to install some missing dependencies.

Maybe this issue is related to bcftools dependencies and tb-profiler doesn't agreeing in the correct htslib=1.15 as bcf requires <=1.11 and tb-profiler requires >=1.15

Thank you for your attention, I'm using tb-profiler since 2.3 and I'm looking forward the new updates!

[jodyphelan]

Thanks @Mxrcon, yeah I'm not sure why this is happening as I thought conda is meant to sort out all the dependencies but I think you are right in saying that the bcftools deps are not agreeing with some of the other software.

What I've done now is add the conda specifications file to the repo (here) and I'll keep that up to date for each version.

[Mxrcon]

Yes! I've identified this error:

conda create -n tb-profiler-test -c bioconda tb-profiler=4.4.0 bcftools=1.12 -y
conda activate tb-profiler-test
bcftools --version

bcftools: symbol lookup error: /home/davi_marcon/miniconda3/envs/tb-profiler-test/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

[jodyphelan]

Interestingly I don't get that error when trying on my system (see attached file). Is it possible something outside of the conda env could have an effect? terminal-log.txt

[Mxrcon]

hmm, maybe yes, what's your operational system? It could be an inconsistency on bcftools installation on some OS

[jodyphelan]

Tested and works on:

• Linux s10 5.4.0-110-generic # 124-Ubuntu SMP Thu Apr 14 19:46:19 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
• Linux PLUM-S3 2.6.32-573.12.1.el6.x86_64 # 1 SMP Tue Dec 15 21:19:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
• Darwin MACB0095 20.2.0 Darwin Kernel Version 20.2.0: Wed Dec 2 20:39:59 PST 2020; root:xnu-7195.60.75~1/RELEASE_X86_64 x86_64

Which version of conda are you running?

[Mxrcon]

Doesn't work on:

• linux 5.15.0-50-generic # 56~20.04.1-Ubuntu SMP Tue Sep 27 15:51:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

Conda version:

• conda 4.12.0