----------------------- Start of variable list: ----------------------- Sample_ID: 3MCA_M1 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/00_Setup_Pipeline BU_User: kkarri VM_DIR_FASTQC: /home/waxmanlab/public_html/FASTQC/CMC_samples OUTPUT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC/Job_Summary ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Jun 9 15:01:16 EDT 2017 Running on node : scc-tm2 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC Current job ID : 9244379 Current job name : Step_02_3MCA_M1 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9244379.1.linga Loading required modules... List files in scratch directory: total 3.6G drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 9 15:01 . drwxrwxrwt. 19 root root 20K Jun 9 15:01 .. drwxr-xr-x 2 kkarri montilab-p 4.0K Jun 9 15:01 3MCA_M1_FASTQC -rw-r--r-- 1 kkarri montilab-p 1.8G Jun 9 15:01 SRR1177997_R1.fastq.gz -rw-r--r-- 1 kkarri montilab-p 1.8G Jun 9 15:01 SRR1177997_R2.fastq.gz Starting to run my commands Unzip files: Finished unzipping Print first 20 lines of FASTQ file: ==> SRR1177997_R1.fastq <== @SRR1177997.1 1 length=101 AATCTTTTGGGGTCCCCTAAAATAAAGAAAGGCATGTCTCCACACTGTAACGGCAGTGATTGTGGATATTCATCTAGCATGGAAGGAAGTGAGACAGGTTC +SRR1177997.1 1 length=101 CCCFFFFFGGHHHHIJJIGJIIJIGIGIJIIIJJJJIJJIJHIEGGGHIJEIJJGIGGGHHCEDEEDFFEEE:CCCDDCDCBDCDDBC@@CCCACCDD4@@ @SRR1177997.2 2 length=101 GTCAAGGTAATCTCTGGCTTCCCTTCAGGACTCTTCATGGTGATGTTCTCCATCATCTCCATGGACTTCTTCCAGCTGGAGGCTGCACAGGCTGGCCGCCG +SRR1177997.2 2 length=101 =;@ABD;BBDFD,C@GFIII;FBDD?@C?ACD@#### @SRR1177997.4 4 length=101 CTTGCTGGAGGGAAAAAAACATCAGTGTCTTTGTTGCCAAGATGAGGAGTGGCTTCTGGCCTGCTCTGCAAATGAACTGGAGGATGTGGACACCCTTACAG +SRR1177997.4 4 length=101 CCCFFFFFHHHHHJJJJJJJJJJJJHIIJJJIIIIIGIJJJIIJIJJGIHFHIJHGGCEEFCDFCE@@CCCCAACCC@AC>,8(5@>@A:CC?BBDCCDCC @SRR1177997.5 5 length=101 GGAAGCCAATGTGAGACTGTGCAGTTGTCTCCCCTTGCCTTGGTCTTCATGGGGTAGAGTGTCCCTTCCCAGTATGCCATCACAGAGGACAGCAGGGCAGA +SRR1177997.5 5 length=101 CCCFFFFFHHHCFHIJJJJJIJJJJJJIJJJJJJJJJJJIJJJGHIJJJJJIJJGHIJJCGGIJIJJJIJJIHGHGHHFFFFFFEEEDEDDDD?AADBDBB ==> SRR1177997_R2.fastq <== @SRR1177997.1 1 length=101 TCCCGAGAACCTGTCTCACTTCCTTCCATGCTAGATGAATATCCACAATCACTGCCGTTACAGTGTGGAGACATGCCTTTCTTTATTTTAGGGGACCCCAA +SRR1177997.1 1 length=101 CCCFFFFFGGHHHJJHHIIIJJJJJJJJIJIJIIJJIIIJJJFGGHIJIFGHEGEHIIIJGGIIJIIJHHHHFFFFFFEECEEEDDCEDD?;**BDCDE:FGD:8@)4;'957.6@(>C=A?######################## @SRR1177997.3 3 length=101 CTTCACGTAACTATGTGGTCCTTTCCCTTCGAAAGAGGAAGGATGTTTAAAAGAGCCTCCGATTCTATCCCACAGTGTGAAGTACTGCCCATAGTTATAGT +SRR1177997.3 3 length=101 CCCFFFFFHGHHGJJJJJHIIIJJJJJJJJIIIJJJJJIJIJGGHGHJJJIJJJJIJJJJJJJJHHHHHGFFFFECECEEECCDDECDDDCCDDDFEEEDC @SRR1177997.4 4 length=101 CTGACATGTTGGCAAAGAGCACCCGGAACTGCAAGGGCACATAGTTGATGTTGATGAACTGTAAGGGTGTCCACATCCTCCAGTTCATTTGCAGAGCAGGC +SRR1177997.4 4 length=101 CCCFFFFFHHHHHJJJJJJIIJJJJJJJJJJJJJJJJIJJIJJJGHIIJJJIHIIJJJJJJHIIHHH?EFFFFECEEEDDDDDCDDEEFDEDDDDDDDDDD @SRR1177997.5 5 length=101 GTAGCTGGCTGGTATCACCTCTGCAGCCAGGAGGACAGAGAAGATGGCCTTCATTGCAGCTTTGGGGCTCTTGATGGCAGGGATCTGCCCTGCTGTCCTCT +SRR1177997.5 5 length=101 CBCFFFFFHGHHFHJIJJJIJJGIJJGIIJJGIJIJJIIIIJIJIIJDIIFHJIHIIGHIIJIIJJHHFFFFEEEEEDDDDB<<@AC@CBCBD4@>CAACC Starting FASTQC command Processing SRR1177997_R1.fastq Printing command: fastqc --outdir SRR1177997_R1.fastq Analysis complete for SRR1177997_R1.fastq Processing SRR1177997_R2.fastq Printing command: fastqc --outdir SRR1177997_R2.fastq Analysis complete for SRR1177997_R2.fastq Finished FASTQC command Copy output to storage dir List files in scratch total 11G drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 9 15:03 . drwxrwxrwt. 16 root root 20K Jun 9 15:08 .. drwxr-xr-x 2 kkarri montilab-p 4.0K Jun 9 15:08 3MCA_M1_FASTQC -rw-r--r-- 1 kkarri montilab-p 5.3G Jun 9 15:01 SRR1177997_R1.fastq -rw-r--r-- 1 kkarri montilab-p 5.3G Jun 9 15:01 SRR1177997_R2.fastq ========================================================== Finished on : Fri Jun 9 15:08:27 EDT 2017 0 hours, 7 minutes and 11 seconds elapsed. ==========================================================