Wed 14 Jul 2021 10:13:13 PM EDT ; Analyzing system WT_LPS1
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'WT_LPS1/QC-LOG'
Wed 14 Jul 2021 10:13:13 PM EDT ; a. ---> Check read quality using FASTQC: results are stored to WT_LPS1/QC-LOG
Wed 14 Jul 2021 10:13:13 PM EDT ; 	       FASTQC logs are written to WT_LPS1/QC-LOG/Log.out
Wed 14 Jul 2021 10:17:31 PM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'WT_LPS1/STAR'
Wed 14 Jul 2021 10:17:31 PM EDT ; b. ---> Running STAR aligner 
Wed 14 Jul 2021 10:17:31 PM EDT ;  STAR logs are written to WT_LPS1/STAR/Log.out
Wed 14 Jul 2021 10:42:59 PM EDT ;   Completed STAR alignment
 
 
Wed 14 Jul 2021 10:42:59 PM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Wed 14 Jul 2021 10:43:59 PM EDT ; c2. ---> Sorting primary BAM
Wed 14 Jul 2021 10:44:19 PM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Wed 14 Jul 2021 10:44:21 PM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'WT_LPS1/BIGWIG'
Wed 14 Jul 2021 10:44:21 PM EDT ; d. ---> Convering to BAM to bigwig
Wed 14 Jul 2021 10:56:22 PM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'WT_LPS1/STRINGTIE'
Wed 14 Jul 2021 10:56:22 PM EDT ; e. ---> Running stringtie assembler with reference annotation
Wed 14 Jul 2021 10:56:51 PM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'WT_LPS1/CUFFLINKS'
Wed 14 Jul 2021 10:56:51 PM EDT ; f. ---> Running cufflinks on WT_LPS1
   Completed cufflinks assembly
 
 
mkdir: created directory 'WT_LPS1/CUFFQUANT'
Wed 14 Jul 2021 10:59:42 PM EDT ; g. ---> Running cuffquant on WT_LPS1
Wed 14 Jul 2021 11:02:08 PM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'WT_LPS1/CUFFNORM'
Wed 14 Jul 2021 11:02:08 PM EDT ; h. ---> Running cuffnorm on WT_LPS1
Wed 14 Jul 2021 11:02:44 PM EDT ;   Completed cuffnorm
 
 
Wed 14 Jul 2021 11:02:44 PM EDT ; completed analysis for system : WT_LPS1