Wed 14 Jul 2021 07:23:05 PM EDT ; Analyzing system KO_NA3
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'KO_NA3/QC-LOG'
Wed 14 Jul 2021 07:23:05 PM EDT ; a. ---> Check read quality using FASTQC: results are stored to KO_NA3/QC-LOG
Wed 14 Jul 2021 07:23:05 PM EDT ; 	       FASTQC logs are written to KO_NA3/QC-LOG/Log.out
Wed 14 Jul 2021 07:28:00 PM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'KO_NA3/STAR'
Wed 14 Jul 2021 07:28:00 PM EDT ; b. ---> Running STAR aligner 
Wed 14 Jul 2021 07:28:00 PM EDT ;  STAR logs are written to KO_NA3/STAR/Log.out
Wed 14 Jul 2021 07:48:52 PM EDT ;   Completed STAR alignment
 
 
Wed 14 Jul 2021 07:48:52 PM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Wed 14 Jul 2021 07:50:00 PM EDT ; c2. ---> Sorting primary BAM
Wed 14 Jul 2021 07:50:17 PM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Wed 14 Jul 2021 07:50:18 PM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'KO_NA3/BIGWIG'
Wed 14 Jul 2021 07:50:18 PM EDT ; d. ---> Convering to BAM to bigwig
Wed 14 Jul 2021 08:01:57 PM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'KO_NA3/STRINGTIE'
Wed 14 Jul 2021 08:01:57 PM EDT ; e. ---> Running stringtie assembler with reference annotation
Wed 14 Jul 2021 08:02:25 PM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'KO_NA3/CUFFLINKS'
Wed 14 Jul 2021 08:02:25 PM EDT ; f. ---> Running cufflinks on KO_NA3
   Completed cufflinks assembly
 
 
mkdir: created directory 'KO_NA3/CUFFQUANT'
Wed 14 Jul 2021 08:04:59 PM EDT ; g. ---> Running cuffquant on KO_NA3
Wed 14 Jul 2021 08:07:13 PM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'KO_NA3/CUFFNORM'
Wed 14 Jul 2021 08:07:13 PM EDT ; h. ---> Running cuffnorm on KO_NA3
Wed 14 Jul 2021 08:07:49 PM EDT ;   Completed cuffnorm
 
 
Wed 14 Jul 2021 08:07:49 PM EDT ; completed analysis for system : KO_NA3