TBProfiler

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lineage fields on tb_profiler uutput?

1

Will someone please explain what the "main_lin", "sub_lin" and "lin" fields mean in the output ? Is it possible to have a case where the main_lin and sub_lin fields are...

robertwhbaldwin

Rv0678 and mmpR5 on report file

1

Hi @jodyphelan! I've been using the JSON output and parsing it out for downstream validation of the results and I came across something that I found a bit odd. I'm...

cimendes

potential issue with lineage typing

1

Dear Jody, I came across some strange results for a SRA sample (ERR4797559) which is supposed to be part of the lineage 1.2.2 according to the tb-profiler website and confirmed...

rderelle

My version is 4.3 and when I execute tb-profiler update_tbdb, the following message appears

3

Running command: set -u pipefail; git checkout master Running command: set -u pipefail; git pull Running command: set -u pipefail; tb-profiler create_db --load Traceback (most recent call last): File "/home/seq/anaconda3/envs/tb4_3_copy/bin/tb-profiler",...

jzhone

problems installing Tb-profiler using conda with MacOS

6

Before start the installation, conda was activated and then I configured the channels: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge After that...

Leobpfbac

AttributeError: 'Namespace' object has no attribute 'conf'

3

Hi @jodyphelan On TBprofiler version 4.4.1, when I created a custom database, the following errors occurred. I can't resove it ,could you please give some help? Thank you! (TBprofiler_4.4.1_old) [huihuigogo@login01...

huihuigogo

OSError: [Errno 18] Invalid cross-device link:

5

tb-profiler 4.4.1 has "OSError: [Errno 18] Invalid cross-device link" error. Same error has been fixed in ntm-profiler.

yujun2017

"Invalid literal for int() with base 10: '.'" Error

10

Hey, I am desperately looking for a command line tool predicting mycobacterium lineages to integrate into my own pipeline (master thesis related). I thought TBProfiler might be the one but...

adriandrr

error running tb profile

1

This is the error report generated while running tb-profile. can you give us pointers on how to fix it. NB: Our read is not paired. tb-profiler profile -1 ERR4403535.fastq Traceback...

AishaBell

Error while running TBprofiler ver. 4.3.0

17

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...

ryobon-dev