TBProfiler

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ValueError: Cant find programs: trimmomatic

3

Hi Jody, I used "mamba create -n tb-profiler tb-profiler" to install tb-profiler v4.3.0. I ran "tb-profiler profile -1 SJ_2012_0029_R1.fastq.gz -2 SJ_2012_0029_R2.fastq.gz -p SJ_2012_0029", and I got Traceback (most recent call...

limengfdu

set -u pipefail; trimmomatic

2

Hi Jody, I get this error while running profiler: set -u pipefail; trimmomatic PE -threads 1 -phred33 /tmp/flytek_8nxtt7/local_flytekit/dd7a9c79cfb126a676d84d21f5aebf89/ERR3077930_1.fastq /tmp/flytek_8nxtt7/local_flytekit/e80258887acb296b57e61d96d65e4c00/ERR3077930_2.fastq -baseout .//root/tbprofiler/pfiles LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36 Command Failed! Please Check!= How...

odetteg

Lineage family missing in text report

7

Dear Jody, I noticed that in v4.2.0 the lineage family is missing in the text report: ``` Summary ------- ID: xxx Date: Sun Jul 3 14:15:29 2022 Strain: lineage2.2.1 Drug-resistance:...

pmenzel

Error while running tb-profile on BAM file

3

i got the following error while running tb-profile on a BAM file Using gff file: /home/st1compgen/anaconda3/envs/tb-profiler/share/tbprofiler/tbdb.gff Using ref file: /home/st1compgen/anaconda3/envs/tb-profiler/share/tbprofiler/tbdb.fasta Using ann file: /home/st1compgen/anaconda3/envs/tb-profiler/share/tbprofiler/tbdb.ann.txt Using barcode file: /home/st1compgen/anaconda3/envs/tb-profiler/share/tbprofiler/tbdb.barcode.bed Using bed...

antonioia9

issue with tb-profiler + conda (+snakemake)

2

This is a fringe issue that I ran into when running TB-profiler through a conda installation that is shared by multiple users. I just want to write it down for...

pmenzel

Mixed infection profiling

1

### Summary Mixed infections can cause difficulties when analysing wgs data. Improved support for mixed infection data as well as mutation phasing will be implemented.

jodyphelan

Bugs when using vcf profile on lofreq output

1

Hi Jody When running TBProfiler (using --vcfprofile) on data generated by lofreq, the frequencies of the variants are computed incorrectly. If there are two variants on the same positions (see...

LennertVerboven

### Summary There is currently no support for generating reports based on longitudinal data. An new module will be developed to look characterise lineage and drug resistance patterns between sequential...

jodyphelan

### Summary A new data extraction module will be build for more flexible and customisible generation of reports as well filtering and searching across multiple results.

jodyphelan