Thu 15 Jul 2021 01:10:29 AM EDT ; Analyzing system WT_NA2
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'WT_NA2/QC-LOG'
Thu 15 Jul 2021 01:10:29 AM EDT ; a. ---> Check read quality using FASTQC: results are stored to WT_NA2/QC-LOG
Thu 15 Jul 2021 01:10:29 AM EDT ; 	       FASTQC logs are written to WT_NA2/QC-LOG/Log.out
Thu 15 Jul 2021 01:14:00 AM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'WT_NA2/STAR'
Thu 15 Jul 2021 01:14:00 AM EDT ; b. ---> Running STAR aligner 
Thu 15 Jul 2021 01:14:00 AM EDT ;  STAR logs are written to WT_NA2/STAR/Log.out
Thu 15 Jul 2021 01:38:24 AM EDT ;   Completed STAR alignment
 
 
Thu 15 Jul 2021 01:38:24 AM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Thu 15 Jul 2021 01:39:16 AM EDT ; c2. ---> Sorting primary BAM
Thu 15 Jul 2021 01:39:35 AM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Thu 15 Jul 2021 01:39:36 AM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'WT_NA2/BIGWIG'
Thu 15 Jul 2021 01:39:36 AM EDT ; d. ---> Convering to BAM to bigwig
Thu 15 Jul 2021 01:50:03 AM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'WT_NA2/STRINGTIE'
Thu 15 Jul 2021 01:50:03 AM EDT ; e. ---> Running stringtie assembler with reference annotation
Thu 15 Jul 2021 01:50:33 AM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'WT_NA2/CUFFLINKS'
Thu 15 Jul 2021 01:50:33 AM EDT ; f. ---> Running cufflinks on WT_NA2
   Completed cufflinks assembly
 
 
mkdir: created directory 'WT_NA2/CUFFQUANT'
Thu 15 Jul 2021 01:53:19 AM EDT ; g. ---> Running cuffquant on WT_NA2
Thu 15 Jul 2021 01:55:48 AM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'WT_NA2/CUFFNORM'
Thu 15 Jul 2021 01:55:48 AM EDT ; h. ---> Running cuffnorm on WT_NA2
Thu 15 Jul 2021 01:56:23 AM EDT ;   Completed cuffnorm
 
 
Thu 15 Jul 2021 01:56:23 AM EDT ; completed analysis for system : WT_NA2