----------------------- Start of variable list: ----------------------- Sample_ID: G123_M9 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env/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_Env/Scripts/02_FASTQC/Job_Summary ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Dec 21 10:30:26 EST 2018 Running on node : scc-kb7 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC Current job ID : 471782 Current job name : Step_02_G123_M9 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/471782.1.linga Loading required modules... List files in scratch directory: total 1.6G drwx------ 3 kkarri waxmanlab 4.0K Dec 21 10:30 . drwxrwxrwt. 25 root root 168K Dec 21 10:30 .. -rw-r----- 1 kkarri waxmanlab 784M Dec 21 10:30 G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq.gz -rw-r----- 1 kkarri waxmanlab 810M Dec 21 10:30 G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq.gz drwxr-xr-x 2 kkarri waxmanlab 4.0K Dec 21 10:30 G123_M9_FASTQC Starting to run my commands Unzip files: Finished unzipping Print first 20 lines of FASTQ file: ==> G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq <== @HWI-D00311:109:C8TK0ANXX:8:1101:1438:2178 1:Y:0:GATCAG GTGAGCTGGGGCTGCAGCATCTTCTCCTCTGGATGCCTAGCCCTGCCAAT + AA=?AE;1B///=FEGFFGGGFG>1=:BF1?1>CG1F1FFD1B=FGB?1: @HWI-D00311:109:C8TK0ANXX:8:1101:1556:2038 1:N:0:GATCAG NTGGCACTCAAAATAAAAAAATAAGATCTGTTAAAAAGTTAAACTGACTG + #<FGC>FGG1FB::CFG11///FECGGGGGGGG1FGGGGGF@:>FF1:C @HWI-D00311:109:C8TK0ANXX:8:1101:1671:2160 1:N:0:GATCAG TGGCCTTCTAGAATCTCTTCCATGGTCTTGCCCTTTGCTCCCAGGGACAC + BBBB@FGG>D1FGGDFGGCFGGEG1C:B@D>GC1CEDEFGGE@>F/0EFG ==> G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq <== @HWI-D00311:109:C8TK0ANXX:8:1101:1438:2178 2:Y:0:GATCAG CTGCAATGGACTTCCGGATCCCCATGCTGGAGTCTATTCCCTGATGGACC + BB=BBG1=11@1==F/==/EF@01:1E1FCGBFGGGG@GGGEEG1FGGG@ @HWI-D00311:109:C8TK0ANXX:8:1101:1556:2038 2:N:0:GATCAG GAAAAATCAAATGTATGATTTATGAAACAAGTGTGTGATGTGTAACTTCA + CCBCCGGGGGGGGGGGGGGGGGGGGGGGGGG>FGGGGGGGGGGGGGGGGG @HWI-D00311:109:C8TK0ANXX:8:1101:1616:2073 2:N:0:GATCAG GTTGAATTCCCCTCTGCTGATTATGTATTTTGGGCCCTGATTTGCTGTCA + ABBBBGGGGGGGGGGGGG=FGFFGGDCBFGGGGABBGGGBGGGGB@1:EGGGGGGGGGGGEGEFGDGGGGEGEGGGGGGCB @HWI-D00311:109:C8TK0ANXX:8:1101:1671:2160 2:N:0:GATCAG ATCAGGAGTCAGCTATCACAGAGGCTCTGCAGCCTGGAGAACAGAGAAGA + B3ABBF@/=CFGGGEGCFGFGGGBD0:1ECDFGE>FG>EGG1CFFEGGBF Starting FASTQC command Processing G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq Printing command: fastqc --outdir G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq Analysis complete for G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq Processing G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq Printing command: fastqc --outdir G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq Analysis complete for G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq Finished FASTQC command Copy output to storage dir List files in scratch total 5.4G drwx------ 3 kkarri waxmanlab 4.0K Dec 21 10:31 . drwxrwxrwt. 27 root root 168K Dec 21 10:36 .. -rw-r----- 1 kkarri waxmanlab 2.7G Dec 21 10:30 G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R1.fastq -rw-r----- 1 kkarri waxmanlab 2.7G Dec 21 10:30 G123-pool-GATCAG_GATCAG_BC8TK0ANXX_L008_001.R2.fastq drwxr-xr-x 2 kkarri waxmanlab 4.0K Dec 21 10:36 G123_M9_FASTQC ========================================================== Finished on : Fri Dec 21 10:36:23 EST 2018 0 hours, 5 minutes and 57 seconds elapsed. ==========================================================