Thu 15 Jul 2021 12:36:55 AM EDT ; Analyzing system WT_NA1
Forward sequence file has been detected. Running analysis in single_end mode 
mkdir: created directory 'WT_NA1/QC-LOG'
Thu 15 Jul 2021 12:36:55 AM EDT ; a. ---> Check read quality using FASTQC: results are stored to WT_NA1/QC-LOG
Thu 15 Jul 2021 12:36:55 AM EDT ; 	       FASTQC logs are written to WT_NA1/QC-LOG/Log.out
Thu 15 Jul 2021 12:38:56 AM EDT ;         Completed FASTQC Analysis
 
 
mkdir: created directory 'WT_NA1/STAR'
Thu 15 Jul 2021 12:38:56 AM EDT ; b. ---> Running STAR aligner 
Thu 15 Jul 2021 12:38:56 AM EDT ;  STAR logs are written to WT_NA1/STAR/Log.out
Thu 15 Jul 2021 12:55:00 AM EDT ;   Completed STAR alignment
 
 
Thu 15 Jul 2021 12:55:00 AM EDT ; c1. ---> Extracting primary reads from the aligned bam file
Thu 15 Jul 2021 12:55:40 AM EDT ; c2. ---> Sorting primary BAM
Thu 15 Jul 2021 12:55:51 AM EDT ; c3. ---> Generating Index for PCR duplicate free sorted BAM
Thu 15 Jul 2021 12:55:52 AM EDT ;   Completed BAM file generation
 
 
mkdir: created directory 'WT_NA1/BIGWIG'
Thu 15 Jul 2021 12:55:52 AM EDT ; d. ---> Convering to BAM to bigwig
Thu 15 Jul 2021 01:05:22 AM EDT ;   Completed conversion to bigwig
 
 
mkdir: created directory 'WT_NA1/STRINGTIE'
Thu 15 Jul 2021 01:05:22 AM EDT ; e. ---> Running stringtie assembler with reference annotation
Thu 15 Jul 2021 01:05:47 AM EDT ;   Completed stringtie assembly
 
 
mkdir: created directory 'WT_NA1/CUFFLINKS'
Thu 15 Jul 2021 01:05:47 AM EDT ; f. ---> Running cufflinks on WT_NA1
   Completed cufflinks assembly
 
 
mkdir: created directory 'WT_NA1/CUFFQUANT'
Thu 15 Jul 2021 01:08:04 AM EDT ; g. ---> Running cuffquant on WT_NA1
Thu 15 Jul 2021 01:09:53 AM EDT ;   Completed cuffquant
 
 
mkdir: created directory 'WT_NA1/CUFFNORM'
Thu 15 Jul 2021 01:09:53 AM EDT ; h. ---> Running cuffnorm on WT_NA1
Thu 15 Jul 2021 01:10:29 AM EDT ;   Completed cuffnorm
 
 
Thu 15 Jul 2021 01:10:29 AM EDT ; completed analysis for system : WT_NA1