Difference between results of installed tbprofiler pipeline and online version

[RehmanZaira]

Hi,
I am analyzing the same data through installed tbprofiler and the online version. I got the Delamanid resistance when using the online version. The version of tbprofier that I am using is 5.0.1.
I am trying to update the tbprofiler but got an error
(env_tbprofiler) ngs@ngs-srv:~$ tb-profiler update_tbdb
[10:43:09] ERROR Traceback (most recent call last): utils.py:391
File
"/home/ngs/miniconda3/envs/env_tbprofiler/bin/t
b-profiler", line 562, in
args.func(args)
File
"/home/ngs/miniconda3/envs/env_tbprofiler/bin/t
b-profiler", line 205, in main_create_db
pp.create_db(args,extra_files=extra_files)
File
"/home/ngs/miniconda3/envs/env_tbprofiler/lib/p
ython3.10/site-packages/pathogenprofiler/db.py"
, line 417, in create_db
hgvs_variants = [r for r in
csv.DictReader(open(args.csv))]
FileNotFoundError: [Errno 2] No such file or
directory: 'tbdb.csv'
Cleaning up after failed run

Traceback (most recent call last):
File "/home/ngs/miniconda3/envs/env_tbprofiler/bin/tb-profiler", line 562, in
args.func(args)
File "/home/ngs/miniconda3/envs/env_tbprofiler/bin/tb-profiler", line 183, in main_update_tbdb
pp.run_cmd(f"tb-profiler create_db --prefix {args.prefix} {tmp} --load")
File "/home/ngs/miniconda3/envs/env_tbprofiler/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 392, in run_cmd
raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))
ValueError: Command Failed:
/bin/bash -c set -o pipefail; tb-profiler create_db --prefix tbdb --load
stderr:
Traceback (most recent call last):
File "/home/ngs/miniconda3/envs/env_tbprofiler/bin/tb-profiler", line 562, in
args.func(args)
File "/home/ngs/miniconda3/envs/env_tbprofiler/bin/tb-profiler", line 205, in main_create_db
pp.create_db(args,extra_files=extra_files)
File "/home/ngs/miniconda3/envs/env_tbprofiler/lib/python3.10/site-packages/pathogenprofiler/db.py", line 417, in create_db
hgvs_variants = [r for r in csv.DictReader(open(args.csv))]
FileNotFoundError: [Errno 2] No such file or directory: 'tbdb.csv'
Cleaning up after failed run

Cleaning up after failed run
ERROR tb-profiler:58

                ################################# ERROR                     
                #######################################                     
                                                                            
                This run has failed. Please check all                       
                arguments and make sure all input files                     
                exist. If no solution is found, please open                 
                up an issue at                                              
                https://github.com/jodyphelan/TBProfiler/issu               
                es/new and paste or attach the                              
                contents of the error log (tbdb.errlog.txt)                 
                                                                            
                #############################################               
                ##################################                          

Kindly guide me how to fix that issue.

[RehmanZaira]

Hi Jody,
I am waiting for your response.

[jodyphelan]

Hi @RehmanZaira ,

There are some incompatabilities between the database repository and older versions of tb-profiler. The easiest fix for this would be to update to use the latest version of tb-profiler. Let me know if this works for you

[RehmanZaira]

Hi @jodyphelan,
I have installed the updated version of tb-profiler 6.5.0. I have the data of sample that was run previously on web version a month ago. When I run the same sample on the updated version i found discrepancy in the Delamanid resistance. Previously it was deletion in fbic gene and in the current version it is in fbib gene and it is gain of stop codon. Can you please tell me which reference genome is used in the current version as the previous version uses H37rv?

[jodyphelan]

There is an issue with the variant calling process which places a deletion in fbiC (see #344). In recent versions this has been corrected, so you should use the results from the more recent version. The same version of the reference genome has been used.

[RehmanZaira]

Thank you for the clarification. In the new version of Tb-profiler, I didn't get any vcf files. The vcf folder is empty.

[jodyphelan]

What was the command you used to run the pipeline?

[RehmanZaira]

HI @jodyphelan when I run the new version of tbprofiler, I didn't get any .vcf files in the vcf folder.

[jodyphelan]

Which options did you use when run run the tb-profiler command?