Wed 14 Jul 2021 11:46:16 PM EDT ; Analyzing system WT_LPS3
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'WT_LPS3/QC-LOG'
Wed 14 Jul 2021 11:46:16 PM EDT ; a. ---> Check read quality using FASTQC: results are stored to WT_LPS3/QC-LOG
Wed 14 Jul 2021 11:46:16 PM EDT ; 	       FASTQC logs are written to WT_LPS3/QC-LOG/Log.out
Wed 14 Jul 2021 11:51:18 PM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'WT_LPS3/STAR'
Wed 14 Jul 2021 11:51:18 PM EDT ; b. ---> Running STAR aligner 
Wed 14 Jul 2021 11:51:18 PM EDT ;  STAR logs are written to WT_LPS3/STAR/Log.out
Thu 15 Jul 2021 12:17:12 AM EDT ;   Completed STAR alignment
 
 
Thu 15 Jul 2021 12:17:12 AM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Thu 15 Jul 2021 12:20:51 AM EDT ; c2. ---> Sorting primary BAM
Thu 15 Jul 2021 12:21:21 AM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Thu 15 Jul 2021 12:21:22 AM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'WT_LPS3/BIGWIG'
Thu 15 Jul 2021 12:21:22 AM EDT ; d. ---> Convering to BAM to bigwig
Thu 15 Jul 2021 12:30:38 AM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'WT_LPS3/STRINGTIE'
Thu 15 Jul 2021 12:30:38 AM EDT ; e. ---> Running stringtie assembler with reference annotation
Thu 15 Jul 2021 12:31:08 AM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'WT_LPS3/CUFFLINKS'
Thu 15 Jul 2021 12:31:08 AM EDT ; f. ---> Running cufflinks on WT_LPS3
   Completed cufflinks assembly
 
 
mkdir: created directory 'WT_LPS3/CUFFQUANT'
Thu 15 Jul 2021 12:33:52 AM EDT ; g. ---> Running cuffquant on WT_LPS3
Thu 15 Jul 2021 12:36:19 AM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'WT_LPS3/CUFFNORM'
Thu 15 Jul 2021 12:36:19 AM EDT ; h. ---> Running cuffnorm on WT_LPS3
Thu 15 Jul 2021 12:36:55 AM EDT ;   Completed cuffnorm
 
 
Thu 15 Jul 2021 12:36:55 AM EDT ; completed analysis for system : WT_LPS3