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stanikae / jekesa

Jekesa (Illuminate) is an automated bash pipeline for bacterial whole genome assembly and typing using Illumina paired-end sequencing data.
https://github.com/stanikae/jekesa
GNU General Public License v3.0
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jekesa fastq #3

Open tauqeer9 opened 2 years ago

tauqeer9 commented 2 years ago

Hello I am trying to run jekesa on S. pneumoniae samples. It works fine at fastqc, assembly and MLST steps (step01, step02, step03 and step05), but all other steps just create empty output file. Looks like it has something to do with my fastq file name/path. Right now my fastq files (Sample1_R1_1.fastq.gz, Sample1_R2_1.fastq.gz) are in a directory callled "FASTQ".

stanikae commented 2 years ago

Hi @tauqeer9 The steps for comprehensive analysis of S. pneumoniae and S. pyogenes are currently broken due to an environment issue for some of the dependencies. Whilst i look into this, could you upload your assemblies to PathogenWatch, for the extensive characterization of your S. pneumoniae isolates.