Cannot perform lineage and spoligotype in v6.2.1

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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Cannot perform lineage and spoligotype in v6.2.1 #365

Open thanadon1437 opened 1 month ago

thanadon1437 commented 1 month ago

Hi Jody,

I just updated the tb-profiler to v6.2.1 and the error about lineage prediction seems resolved but there is no result about lineage in the .json file (it shows ""). The spoligotype also got the error that I attached a log file here.

Screen Shot 2567-05-24 at 10 17 43 AM

bc34spo.errlog.txt

also the .bam file if you want to test it yourself. barcode34-2.zip

jodyphelan commented 1 month ago

Hi @thanadon1437

I believe this is targeted NGS data right? In this case the lineage prediction won't work as it uses SNPs that are not covered by the amplicons. The Spoligotype bug is fixed in the latest version and should be available in v6.2.2 when it comes out.

thanadon1437 commented 1 month ago

Hi @thanadon1437

I believe this is targeted NGS data right? In this case the lineage prediction won't work as it uses SNPs that are not covered by the amplicons. The Spoligotype bug is fixed in the latest version and should be available in v6.2.2 when it comes out.

Thank you @jodyphelan

Yes, it is targeted NGS data. Will it be improved in the next version? because I used the built-in software from ONT they can report the lineage like this while TB-profiler cannot report the lineage in the same sample.

TB-profiler result