----------------------- Start of variable list: ----------------------- Sample_ID: 3_Liver_High_3h Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741 Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/00_Setup_Pipeline BU_User: varsha97 VM_DIR_FASTQC: /net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE117741 OUTPUT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC/Job_Summary ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Jul 3 11:57:37 EDT 2019 Running on node : scc-ka4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC Current job ID : 7500905 Current job name : Step_02_3_Liver_High_3h Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/7500905.1.linga Loading required modules... List files in scratch directory: total 631M drwx------ 3 varsha97 waxmanlab 4.0K Jul 3 12:00 . drwxrwxrwt. 11 root root 4.0K Jul 3 11:59 .. drwxr-xr-x 2 varsha97 waxmanlab 4.0K Jul 3 12:00 3_Liver_High_3h_FASTQC -rw-r--r-- 1 varsha97 waxmanlab 301M Jul 3 11:59 SRR7585237_1.fastq.gz -rw-r--r-- 1 varsha97 waxmanlab 330M Jul 3 12:00 SRR7585237_2.fastq.gz Starting to run my commands Unzip files: Finished unzipping Print first 20 lines of FASTQ file: ==> SRR7585237_1.fastq <== @SRR7585237.1 SN363:873:H7VCKBCXX:2:1101:1917:2196/1 ACGGCCTTTACCGCAAGCTGGTCATTAATGACGTGCAGCCTGAGGATAGG + DDDDDIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @SRR7585237.2 SN363:873:H7VCKBCXX:2:1101:2156:2062/1 NGGGGGACTCTGGTGTTGGAAAGACCTCTCTCATGAACCAGTATGTGAGG + #< SRR7585237_2.fastq <== @SRR7585237.1 SN363:873:H7VCKBCXX:2:1101:1917:2196/2 TATCCTCAGGCTGCACGTCATTAATGACCAGCTTGCGGTAAAGGCCGTGA + DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH @SRR7585237.2 SN363:873:H7VCKBCXX:2:1101:2156:2062/2 TCACATACTGGTTCATGAGAGAGGTCTTTCCAACACCAGAGTCCCCCAGA + DDDDDIIIIIHHIIIHIIIHIIIIIIIIIIIHHHIHHHIIIIIIIIIIHH @SRR7585237.3 SN363:873:H7VCKBCXX:2:1101:2367:2059/2 GAAGGAACTAAGGGCAATGCAGTTGGAACAGGTGCTGGGGCGGGGCCAGG + DADDCIHHIGIIIIIHIHIIIIHIIIIHIIIIIIHIIIGIIIIIICHIHI @SRR7585237.4 SN363:873:H7VCKBCXX:2:1101:2303:2149/2 CCAAAAATGCATGCCCTGTAACATGGCATTCAGAACAAAAGGCACATTAT + DDDDDHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @SRR7585237.5 SN363:873:H7VCKBCXX:2:1101:2824:2107/2 TCTATTATGAAGTTAGTTGAGTAGAGTTCTGGTAAATTGATATAGTATAG + DDCDDIHHIIIHHIIIIHHIIIIIHIHIIIIIHIIIIIIIIIIIIIIIIH Starting FASTQC command Processing SRR7585237_1.fastq Printing command: fastqc --outdir SRR7585237_1.fastq Analysis complete for SRR7585237_1.fastq Processing SRR7585237_2.fastq Printing command: fastqc --outdir SRR7585237_2.fastq Analysis complete for SRR7585237_2.fastq Finished FASTQC command Copy output to storage dir List files in scratch total 2.5G drwx------ 3 varsha97 waxmanlab 4.0K Jul 3 12:01 . drwxrwxrwt. 10 root root 4.0K Jul 3 12:01 .. drwxr-xr-x 2 varsha97 waxmanlab 4.0K Jul 3 12:02 3_Liver_High_3h_FASTQC -rw-r--r-- 1 varsha97 waxmanlab 1.3G Jul 3 11:59 SRR7585237_1.fastq -rw-r--r-- 1 varsha97 waxmanlab 1.3G Jul 3 12:00 SRR7585237_2.fastq ========================================================== Finished on : Wed Jul 3 12:02:54 EDT 2019 0 hours, 5 minutes and 17 seconds elapsed. ==========================================================