-----------------------
Start of variable list:
-----------------------
Sample_ID:
NSM_IP2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/home/waxmanlab/public_html/FASTQC/IP_Saline
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jun 14 17:15:49 EDT 2017
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/02_FASTQC
Current job ID : 9321129
Current job name : Step_02_NSM_IP2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9321129.1.linga

Loading required modules...


List files in scratch directory:

total 3.0G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 14 17:15 .
drwxrwxrwt. 177 root   root        84K Jun 14 17:15 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 14 17:15 NSM_IP2_FASTQC
-rw-r--r--    1 kkarri montilab-p 1.5G Jun 14 17:15 SRR1177985_R1.fastq.gz
-rw-r--r--    1 kkarri montilab-p 1.5G Jun 14 17:15 SRR1177985_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177985_R1.fastq <==
@SRR1177985.1 1 length=101
AAAGATCTTGCCGAGAAGAAAAGCAGCGAGGGGCATGATGCCAAACTGGGCCACCAAGGCAACGATCACCCCTTTGGGCTTCCACAAGTGAGCCTTGATCT
+SRR1177985.1 1 length=101
@@@DDFFDHHHGHB@<FHJJJJFAHGGG>HHGGGHIGEIJIJCHGIFEHCEBEFABAEC@AA?;?ABBDCADBBCCC9?C?CACDDDBC:@>CCC@ACDCD
@SRR1177985.2 2 length=101
CCCAACACTAATTATCATTACACGATGAGGCAACCAAACAGAACGCTTAAATGCAGGAATTTATTTCCTGTTTTATACACTAATTGGCTCCATCCCACTCT
+SRR1177985.2 2 length=101
C@CFFFFFHFFFFHGGHHHJGIGHHIGIJJIIJJJJJJIJJJJIIJGIGIFEHIJJIIJIIIEHGFHFHFCDCBFEECCEEECDEDDDDCBDDDBDDDDDD
@SRR1177985.3 3 length=101
CTGGAGAGAAGCAAAGGTGTCTTTGTAGAGGACTGGAATAAAGGCAGGACTATTGATGGGCATCCACAGGGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
+SRR1177985.3 3 length=101
@@CFFFFFHFFDDIJIIHIIIIIDGHGHIJJJJIJJJIJIJIHGHJGIDGGHGIGEGHJJIJIHIJJGA=ADDFDEEEEECCCCCDA@ACDDDDDDDDCD4
@SRR1177985.4 4 length=101
GTGCTGCAGGACTCCCTGGACGCAAAATGAAGAGGGTTCTGGTTCTCCTGCTGGCCTTAGCCTTTGGGCATGCCCTAGAGAGAGGCCGAGATTATGAGAAG
+SRR1177985.4 4 length=101
BBCFFFFFHHFHAGIGIJJJJJIJJJJIEHIIJJIIDFHIJJFHGIIJIIHIGIFJJJIHHHHHHFFFFDEEEEDDDDCDCD@BDDDD@BDDDDDCCDDDC
@SRR1177985.5 5 length=101
CGGACGGGAGCCTCCTCCGCGGGTATATGCAGTATGCCTATGATGGCCGCGATTACATCGCCCTGAACGAAGACCTCAAAACGTGGATGGTGAAGGACACA
+SRR1177985.5 5 length=101
B@CFFFFFHGHHGJJJJJHIJJJFGDGIJIIGIHEHHHHFFFFFFFDEDD;@BDDCDDDDDDDDDDDDDDDBDDDDDDC@@BBABDDDCDA@(:@C<89A9

==> SRR1177985_R2.fastq <==
@SRR1177985.1 1 length=101
CTCTCACTGGGCTGCACCATGGAATTCAGCAAGATCAAGGCTCACTTGTGGAAGCCCAAAGGGNTNATCGTTGCCTTGGTGGCCCAGTTTGGCATCATGCC
+SRR1177985.1 1 length=101
@@@DBDDAFF;;D?CFFBHHGEAEAGDCGGIIFBDGIH:B?BFEEDDB?DDGB9;CGGGIFHG#(#--;;;6;<CE>;.>1?BBDDD>@A58CC>CCA@CC
@SRR1177985.2 2 length=101
TGGNGNNNNNNNNNNNNNGNNAGGATTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTGGGATGGNNNNAANNAGTGN
+SRR1177985.2 2 length=101
C@C##################################################################################################
@SRR1177985.3 3 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SRR1177985.3 3 length=101
#####################################################################################################
@SRR1177985.4 4 length=101
CTNNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGNNNNGANNNNNNNNNNNNNNN
+SRR1177985.4 4 length=101
@@###################################################################################################
@SRR1177985.5 5 length=101
TCTCTCTCCAAAACCAGCCTGATCCCACTTGTTTNNNNNNNNNNNNNNTGCTGTGTCCTNNNNNNNNNNNGTTTTGAGGTCTTCGTTCAGGGCGATGTAAT
+SRR1177985.5 5 length=101
?BCFFFFFHHHHHJIJIFGHIEIIJIJIIJIFIJ##############--7@GFI>EII###########,,5?@B@BDCCCDDDACDDDDBBDBBBACD:

Starting FASTQC command


Processing SRR1177985_R1.fastq

Printing command:
fastqc --outdir SRR1177985_R1.fastq

Analysis complete for SRR1177985_R1.fastq

Processing SRR1177985_R2.fastq

Printing command:
fastqc --outdir SRR1177985_R2.fastq

Analysis complete for SRR1177985_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 8.8G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 14 17:18 .
drwxrwxrwt. 177 root   root        84K Jun 14 17:21 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 14 17:24 NSM_IP2_FASTQC
-rw-r--r--    1 kkarri montilab-p 4.4G Jun 14 17:15 SRR1177985_R1.fastq
-rw-r--r--    1 kkarri montilab-p 4.4G Jun 14 17:15 SRR1177985_R2.fastq
==========================================================
Finished on : Wed Jun 14 17:24:48 EDT 2017
0 hours, 8 minutes and 59 seconds elapsed.
==========================================================