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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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Collate issue #322

Open EtienneNtumba opened 8 months ago

EtienneNtumba commented 8 months ago

b-profiler collate [04:57:16] INFO Using ref file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.fasta db.py:594 INFO Using gff file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.gff db.py:594 INFO Using bed file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.bed db.py:594 INFO Using version file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.version.json db.py:594 INFO Using json_db file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.dr.json db.py:594 INFO Using variables file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.variables.json db.py:594 INFO Using spoligotype_spacers file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.spoligotype_spacers.txt db.py:594 INFO Using spoligotype_annotations file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.spoligotype_list.csv db.py:594 INFO Using bedmask file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.mask.bed db.py:594 INFO Using barcode file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.barcode.bed db.py:594 0%| | 0/1 [00:00<?, ?it/s] Traceback (most recent call last): File "/home/p0129674/anaconda3/envs/my_pro/bin/tb-profiler", line 562, in args.func(args) File "/home/p0129674/anaconda3/envs/my_pro/bin/tb-profiler", line 253, in main_collate tbp.collate_results(args.prefix,args.conf,sample_file=args.samples,result_dirs=args.dir,mark_missing=args.mark_missing) File "/home/p0129674/anaconda3/envs/my_pro/lib/python3.8/site-packages/tbprofiler/collate.py", line 74, in collate_results if "missing_positions" in temp["qc"]: KeyError: 'qc' Cleaning up after failed run ERROR

jodyphelan commented 5 months ago

Hi @EtienneNtumba ,

Can you try replicate this error with the latest version (v6.2.0)? Let me know if it is still an issue.