Open moks-micro opened 1 month ago
jodyphelan
commented
1 month ago Hey Simone!
You can add in --itol to the command. I thought i was the only one who used it so I took it out of the default settings, but maybe I'll but it back in the next version!
moks-micro
commented
1 month ago Thanks Jody!! We really like to use the itol files here :) The only problem when I use --itol is that it seems to have a problem if La1-3 lineages are present and wont create the itol files. It only works when I have lineages 1-5. Does this ever happen to you ?
(tbprofiler_6.2.1) simone@BioinformaticsWorkstation:~/Documents/tbprofiler6.2.1_validation/TBprofiler_6.2.1$ tb-profiler collate -p tbprofiler6.2.1_validation --itol
[09:00:59] INFO Using ref file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.fasta db.py:587
INFO Using gff file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.gff db.py:587
INFO Using bed file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.bed db.py:587
INFO Using json_db file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.dr.json db.py:587
INFO Using variables file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.variables.json db.py:587
INFO Using spoligotype_spacers file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.spoligotype_spacers.txt db.py:587
INFO Using spoligotype_annotations file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.spoligotype_list.csv db.py:587
INFO Using bedmask file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.mask.bed db.py:587
INFO Using barcode file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.barcode.bed db.py:587
INFO Using rules file: /home/simone/miniconda3/envs/tbprofiler_6.2.1/share/tbprofiler//tbdb.rules.txt db.py:587
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 157/157 [00:00<00:00, 448.86it/s]
Traceback (most recent call last):
File "/home/simone/miniconda3/envs/tbprofiler_6.2.1/bin/tb-profiler", line 587, in
################################# 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/issues/new and paste or attach the
contents of the error log (tbprofiler6.2.1_validation.errlog.txt) Oh this looks like a bug. I'll run some tests.
abhi18av
commented
3 weeks ago Hi @jodyphelan ,
Ran across the same behavior, though for a specific sample - we'd like to reenable iTol for v2 of MAGMA and the error highlights Mcanetti for some reason. https://github.com/TORCH-Consortium/MAGMA/pull/197
Traceback (most recent call last):
File "/usr/local/bin/tb-profiler", line 583, in <module>
args.func(args)
File "/usr/local/bin/tb-profiler", line 269, in main_collate
tbp.collate_results(args)
File "/usr/local/lib/python3.10/site-packages/tbprofiler/collate.py", line 149, in collate_results
generate_itol_config(rows,drugs,args.prefix)
File "/usr/local/lib/python3.10/site-packages/tbprofiler/collate.py", line 178, in generate_itol_config
writer.write(lineage_outfile)
File "/usr/local/lib/python3.10/site-packages/itol_config/interfaces/colour_strip.py", line 33, in write
O.write("%s\t%s\n" % (index,self.colour_lookup[value]))
KeyError: 'M.canetti'
Cleaning up after failed run
ERROR tb-profiler:59
################################# 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
(joint.major_variants.errlog.txt)
#############################################
##################################
CC @vrennie @mdediegofuertes
Hi Jody,
I've been running tbprofiler v6.2.1, and it doesn't seem to be creating any of the iTOL files when I run the collate command:
tb-profiler collate -p test_name
Am I missing something in the command ?
Thanks Simone