----------------------- Start of variable list: ----------------------- Sample_ID: LZ_M15 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/00_Setup_Pipeline BU_User: kkarri VM_DIR_FASTQC: /net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/LZ OUTPUT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC/Job_Summary ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri May 11 10:43:48 EDT 2018 Running on node : scc-wf3 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC Current job ID : 6177143 Current job name : Step_02_LZ_M15 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6177143.1.w Loading required modules... List files in scratch directory: total 714M drwx------ 3 kkarri waxmanlab 4.0K May 11 10:43 . drwxrwxrwt. 28 root root 68K May 11 10:43 .. -rw-r--r-- 1 kkarri waxmanlab 714M May 11 10:43 LZ_M15.fastq.gz drwxr-xr-x 2 kkarri waxmanlab 4.0K May 11 10:43 LZ_M15_FASTQC Starting to run my commands Unzip files: Finished unzipping Print first 20 lines of FASTQ file: @SRR6729558.1 SN390:1085:C9V75ACXX:7:1109:1476:1927 length=33 NCGACTTCCATGGCCACCGTCCTGCTGTCTATA +SRR6729558.1 SN390:1085:C9V75ACXX:7:1109:1476:1927 length=33 #1=DDFFFHFFHHJJGHGHEGGHBHIIGIIIID @SRR6729558.2 SN390:1085:C9V75ACXX:7:1109:1693:1965 length=33 TGAATCTTCAAGGACATGGTGTTCACCCGCGCC +SRR6729558.2 SN390:1085:C9V75ACXX:7:1109:1693:1965 length=33 CCCFF?DDDABFFEFGG@F