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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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Running tb-profiler with --call_whole_genome and --snp_dist argument. #406

Closed justicengom closed 12 hours ago

justicengom commented 6 days ago

Hi Jody I ran this "cat samples.txt | parallel --bar -j 2 tb-profiler profile -1 {}_R1.fastq.gz -2 {}_R2.fastq.gz -p {} --txt --call_whole_genome --snp_dist 200" and I got this message R16787_lib18852.errlog.txt R21373_XXX_XXX.errlog.txt thank you

jodyphelan commented 6 days ago

Oh this is due to a change I made in the recipe in the last release. For now you can do mamba install ucsc-fatovcf and I will make add a new script to replace this one in the next release.

justicengom commented 5 days ago

Okay noted Thanks