----------------------- Start of variable list: ----------------------- Sample_ID: G123_M13 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/00_Setup_Pipeline BU_User: kkarri VM_DIR_FASTQC: /net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G123 OUTPUT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/02_FASTQC/Job_Summary ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Dec 7 14:16:03 EST 2018 Running on node : scc-tk2 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/02_FASTQC Current job ID : 24485 Current job name : Step_02_G123_M13 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/24485.1.linga Loading required modules... List files in scratch directory: total 1.8G drwx------ 3 kkarri waxmanlab 4.0K Dec 7 14:16 . drwxrwxrwt. 28 root root 36K Dec 7 14:16 .. -rw-r----- 1 kkarri waxmanlab 883M Dec 7 14:16 G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq.gz -rw-r----- 1 kkarri waxmanlab 915M Dec 7 14:16 G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq.gz drwxr-xr-x 2 kkarri waxmanlab 4.0K Dec 7 14:16 G123_M13_FASTQC Starting to run my commands Unzip files: Finished unzipping Print first 20 lines of FASTQ file: ==> G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq <== @HWI-D00311:109:C8TK0ANXX:8:1101:1426:2132 1:N:0:ATGTCA CTGCTCCACATATCTCAGTTGACCTCTTTCCCTTGGTTGATAAAAACATA + BBBCBGGGGGGGGGGGGGGGGGGGEGGGGGGFGGGGGEGGGGGGGGGGGC @HWI-D00311:109:C8TK0ANXX:8:1101:1494:2136 1:N:0:ATGTCA GAGGAAGCTGGCTGAGCAAAGGCCCAACTCCTTTCATTTCCTGGAGCTGC + CCCABFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGDGG @HWI-D00311:109:C8TK0ANXX:8:1101:1430:2239 1:N:0:ATGTCA ATTAGCTACCTCTTCATAGAAGCCCTGCAGCTGCAAGTTGGCATCAGAAT + CCCCCGGGGGGGFGGGGGFGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGE @HWI-D00311:109:C8TK0ANXX:8:1101:1955:2018 1:N:0:ATGTCA NAGGGCCACACCCTCCAGCTTCTGATCCAGTGTCTTGAGGTCATCGAGGA + #<GGGFGDGGGDGDGGGGGGFGGG ==> G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq <== @HWI-D00311:109:C8TK0ANXX:8:1101:1426:2132 2:N:0:ATGTCA ATAAAGCAGAATGCTCAGTGTTTGCATGGAGACATTGCACAGTCACAAAG + CCBCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGG @HWI-D00311:109:C8TK0ANXX:8:1101:1494:2136 2:N:0:ATGTCA GGAAAGCACTGTGATCCCCATTGCTCCCCAGTTCTGCCTTCTGGATTCAC + CBBBCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG @HWI-D00311:109:C8TK0ANXX:8:1101:1430:2239 2:N:0:ATGTCA ATTGAAATGCTGAACAAGGCCCGAGAGGACCACACTGTCCCAGAGAGGAG + CCCCCGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG @HWI-D00311:109:C8TK0ANXX:8:1101:1955:2018 2:N:0:ATGTCA GGAGAACCTGGCCAAGCTGATCCAGCATGCCAACGTGCAGTCGTACAGCA + BBBBCGGGGGGGGGGGGGGGGGGGGGGGGFGGFGGGGGGGGGGGGGDGGG @HWI-D00311:109:C8TK0ANXX:8:1101:1919:2116 2:N:0:ATGTCA GGCCCCACGGCCGCACAGGCCAAGTCTAAGCAGGCCATCTTAGCGGCTCA + @@BBCGGDGGGG>DDEB@FGGGGGGGGGGEGGGEGGGGGGGGGGGGGAGF Starting FASTQC command Processing G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq Printing command: fastqc --outdir G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq Analysis complete for G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq Processing G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq Printing command: fastqc --outdir G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq Analysis complete for G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq Finished FASTQC command Copy output to storage dir List files in scratch total 6.1G drwx------ 3 kkarri waxmanlab 4.0K Dec 7 14:17 . drwxrwxrwt. 25 root root 36K Dec 7 14:19 .. -rw-r----- 1 kkarri waxmanlab 3.1G Dec 7 14:16 G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R1.fastq -rw-r----- 1 kkarri waxmanlab 3.1G Dec 7 14:16 G123-pool-ATGTCA_ATGTCA_BC8TK0ANXX_L008_001.R2.fastq drwxr-xr-x 2 kkarri waxmanlab 4.0K Dec 7 14:20 G123_M13_FASTQC ========================================================== Finished on : Fri Dec 7 14:20:07 EST 2018 0 hours, 4 minutes and 4 seconds elapsed. ==========================================================