Wed 14 Jul 2021 08:07:49 PM EDT ; Analyzing system WT_GAQ1
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'WT_GAQ1/QC-LOG'
Wed 14 Jul 2021 08:07:49 PM EDT ; a. ---> Check read quality using FASTQC: results are stored to WT_GAQ1/QC-LOG
Wed 14 Jul 2021 08:07:49 PM EDT ; 	       FASTQC logs are written to WT_GAQ1/QC-LOG/Log.out
Wed 14 Jul 2021 08:11:45 PM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'WT_GAQ1/STAR'
Wed 14 Jul 2021 08:11:45 PM EDT ; b. ---> Running STAR aligner 
Wed 14 Jul 2021 08:11:45 PM EDT ;  STAR logs are written to WT_GAQ1/STAR/Log.out
Wed 14 Jul 2021 08:33:22 PM EDT ;   Completed STAR alignment
 
 
Wed 14 Jul 2021 08:33:22 PM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Wed 14 Jul 2021 08:34:09 PM EDT ; c2. ---> Sorting primary BAM
Wed 14 Jul 2021 08:34:25 PM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Wed 14 Jul 2021 08:34:26 PM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'WT_GAQ1/BIGWIG'
Wed 14 Jul 2021 08:34:26 PM EDT ; d. ---> Convering to BAM to bigwig
Wed 14 Jul 2021 08:44:17 PM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'WT_GAQ1/STRINGTIE'
Wed 14 Jul 2021 08:44:17 PM EDT ; e. ---> Running stringtie assembler with reference annotation
Wed 14 Jul 2021 08:44:45 PM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'WT_GAQ1/CUFFLINKS'
Wed 14 Jul 2021 08:44:45 PM EDT ; f. ---> Running cufflinks on WT_GAQ1
   Completed cufflinks assembly
 
 
mkdir: created directory 'WT_GAQ1/CUFFQUANT'
Wed 14 Jul 2021 08:47:23 PM EDT ; g. ---> Running cuffquant on WT_GAQ1
Wed 14 Jul 2021 08:49:41 PM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'WT_GAQ1/CUFFNORM'
Wed 14 Jul 2021 08:49:41 PM EDT ; h. ---> Running cuffnorm on WT_GAQ1
Wed 14 Jul 2021 08:50:16 PM EDT ;   Completed cuffnorm
 
 
Wed 14 Jul 2021 08:50:16 PM EDT ; completed analysis for system : WT_GAQ1