22:01:58 [INFO ]  ===> cp ../sampleData/pathogenRef/mycobacteriumTuberculosis/mycobacteriumTuberculosis.fa ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa
22:01:59 [INFO ]  ===> cp ../sampleData/pathogenRef/mycobacteriumTuberculosis/genes.gbk ../mtuberculosis2/data/mycobacteriumTuberculosis/genes.gbk
22:01:59 [INFO ]  ===> cp ../sampleData/pathogenRef/mycobacteriumTuberculosis/protein.fa ../mtuberculosis2/data/mycobacteriumTuberculosis/protein.fa
22:02:04 [INFO ]  ===> fastq-dump
22:02:04 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
22:02:04 [INFO ]  ===> samtools
22:02:04 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
22:02:05 [INFO ]  ===> ../tools/FastQC/fastqc
22:02:05 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
22:02:06 [INFO ]  ===> bcftools
22:02:06 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
22:02:06 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
22:02:08 [INFO ]  ===> ../tools/hisat2-2.1.0/hisat2 --version
22:02:12 [INFO ]  9 experiments found for project PRJNA1010683.