-----------------------
Start of variable list:
-----------------------
Sample_ID:
PA_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 15:01:17 EDT 2017
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC
Current job ID : 9244393
Current job name : Step_02_PA_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9244393.1.linga

Loading required modules...


List files in scratch directory:

total 3.4G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun  9 15:01 .
drwxrwxrwt. 121 root   root       112K Jun  9 15:01 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun  9 15:01 PA_M1_FASTQC
-rw-r--r--    1 kkarri montilab-p 1.7G Jun  9 15:01 SRR1177963_R1.fastq.gz
-rw-r--r--    1 kkarri montilab-p 1.7G Jun  9 15:01 SRR1177963_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177963_R1.fastq <==
@SRR1177963.1 1 length=101
TGCTAGGTTGGCTAAGCTTGCTAATAGTCATCATGTTGCTATCAATGGAAAGATTATTTGTAATCCTCGGGCTATAATTATAGTTCGGCTGTGGATTCGGT
+SRR1177963.1 1 length=101
@@@FDFDDBFFBDFEHIIJEGCDGGEHHIJGGIHHHEHHJDGEHIIDCBD9BDDB<FDDDFHGII<CHGGHIACHGEEDDFDFAA@?>B=?(:<>@A@###
@SRR1177963.2 2 length=101
CACAAATCCAGAAAGTGAACTTCAGTGCTCTAATGCAAATGGTAAAGCTGTTTCTCTTCTATCTGTAGTTAAAACTGAATTACAATTTTATTTTCCTGATA
+SRR1177963.2 2 length=101
???DADDDD?:2AE:A<C4<AEF9<3ABEBD<?FFI<CEADC*??**0B:::?0B*?B9?<<DE<9BBCEDBBC7=@D:@C:7@7=A3==;C#########
@SRR1177963.3 3 length=101
TTCTGGAATGCTTATAAGTGGCCTGTGGGAGCTGTAAGAAATAACTGGGGGCCATTGGTTTAAGCTTACTGGCTCTGACATGACTAGTGCCTGTCAGCCCA
+SRR1177963.3 3 length=101
@@?DBDBDHH>:<CFH@A<FHHIGHHIFF=B))1?D@?<@;BB<<4*92@F'5;DHDHCEC>77;C3736@@C@>>3;;@A:3:>C3;A5,::5@@#####
@SRR1177963.4 4 length=101
CCTTTGTCAAGCATACAACCATATTTGAGGTTTTGCCACAGAAGGCTGACAGGGATCAATATGAGCTGCTCTGCCTTGACAATACCCGCAAGCCAGTGTAT
+SRR1177963.4 4 length=101
<?@:DDDDFF???CFGEHICHB>ECHICHCG3C?EB9D>GHGI@38DDF3?D?@(=BF@GGCFG7==E9CEC>EHH>>BEDCC;@A;3>?:@98?######
@SRR1177963.5 5 length=101
GGTCGCTATGCCCTGGTGGTCTGTGGTGATATCGCAGTCTACCCAAGTGGTAACGCCCGCCCCACAGGTGGTGCCGGGGCTGTGGCAATGCTGATTGGGCC
+SRR1177963.5 5 length=101
@@@?DDDDAAACFIE;+<;)AEFFGICCHG9G?:BFADHC*BF?DF;BFHIGFCGHG;:A>DABB?@B5:<BBACBBBB>9<?C(8<@CCCC::4>>1<28

==> SRR1177963_R2.fastq <==
@SRR1177963.1 1 length=101
CAGCCATTNNNATCCANACACCATGAAGCTTCANNNNNNNNNNNNNNNTNNNAANCGNNNNNNNNNNNNNNNCCTCACTCTTATTCTGCNTNGCAAACACC
+SRR1177963.1 1 length=101
=?:BD8:D###2+2<C#2+AAAB9CGCHFGEDF####################################################################
@SRR1177963.2 2 length=101
GTGGAAATNNNNCNNNTTTTCCCTCTCNGGAAANNNNNNNNNNNNNNNNNTTNNANNNNNNNNNNNNNNNNNANCAGCTTTAACATTNGNNNTAGAGCACG
+SRR1177963.2 2 length=101
B1BDBDDF####2###2+33<?9<?F?#1:?;B####################################################################
@SRR1177963.3 3 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANANNCCNNNNNNNNNNNNNNN
+SRR1177963.3 3 length=101
#####################################################################################################
@SRR1177963.4 4 length=101
TANTNNNNNNNNNNNNNNNNNNAANTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAAATATNNNNNNANNCNNGNN
+SRR1177963.4 4 length=101
?B###################################################################################################
@SRR1177963.5 5 length=101
CATTNGNNNNNNNNNNNNNNNTAGCACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTCGAAGGNNNNCGNGTNCNN
+SRR1177963.5 5 length=101
?@B##################################################################################################

Starting FASTQC command


Processing SRR1177963_R1.fastq

Printing command:
fastqc --outdir SRR1177963_R1.fastq

Analysis complete for SRR1177963_R1.fastq

Processing SRR1177963_R2.fastq

Printing command:
fastqc --outdir SRR1177963_R2.fastq

Analysis complete for SRR1177963_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.5G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun  9 15:04 .
drwxrwxrwt. 119 root   root       112K Jun  9 15:11 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun  9 15:13 PA_M1_FASTQC
-rw-r--r--    1 kkarri montilab-p 4.8G Jun  9 15:01 SRR1177963_R1.fastq
-rw-r--r--    1 kkarri montilab-p 4.8G Jun  9 15:01 SRR1177963_R2.fastq
==========================================================
Finished on : Fri Jun  9 15:13:39 EDT 2017
0 hours, 12 minutes and 22 seconds elapsed.
==========================================================