-----------------------
Start of variable list:
-----------------------
Sample_ID:
PA_M3
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-ka7
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC
Current job ID : 9244395
Current job name : Step_02_PA_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9244395.1.linga

Loading required modules...


List files in scratch directory:

total 3.2G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun  9 15:02 .
drwxrwxrwt. 99 root   root       340K Jun  9 15:01 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun  9 15:02 PA_M3_FASTQC
-rw-r--r--   1 kkarri montilab-p 1.6G Jun  9 15:01 SRR1177965_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.6G Jun  9 15:02 SRR1177965_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177965_R1.fastq <==
@SRR1177965.1 1 length=101
CAAAGTGGCAACAAATAAGCAAAACCGTATGATCAGATGCTGTCCTTGACTGTCCTCACAGGATCACTATAAAGTCCACTAAACTGTCTCCAACTCTTCTC
+SRR1177965.1 1 length=101
@@@AD=D??DHHHIGEG<+CFHFED=CE=EDDFB4:9BFHGHIE>DHGGIFHDDGIAFGI4;@FGIGIGHFE>>7=ACEE@;@;>A;A@-;AC;;@C>CCC
@SRR1177965.2 2 length=101
AGAAGCCTTAGCCTAAACACATCACAACCATCTCAGGCTACCCTGAGAAAAAAAAAGACATGAAGACTCAGGACTCATCTCTTCTGTTGGTGTAAAACCAA
+SRR1177965.2 2 length=101
=?<?++AADACBDFGEI::CFDGH9FHICC<CDGIEFF>FGFG>FFGFFEEFFEEB<?AA3;>B@A35>ABBBBBABBBA3;5:@:(::<(<+4>4>@<B@
@SRR1177965.3 3 length=101
TGGCTGTAGCGCTCATATGACCCTTCTCGTCCACAGAAAACTCAGCGATGATGTTGTCTTGCAAAAAGAGACCCTCGGGATCCTTTTTGGCGATGGCATAC
+SRR1177965.3 3 length=101
@@@DDDFDBFHHBEHE@C,CHEBA@FBF=?DDGCBH>B<F??FH@?@G24====@D@CDH@)7?AAHDFD@3=B@;@DB?B?<>AC<A#############
@SRR1177965.4 4 length=101
CACCAGTGCTGTCCTGGCGGCGGCTACTTCGGCACGGCGGGTAACTTCATGGAATGTCAGCCTGAGTGGAAGATCTCTCATCGGTTCCATAAGGACTGTGC
+SRR1177965.4 4 length=101
::?71D=A42A<?:,2+C<):@0@A############################################################################
@SRR1177965.5 5 length=101
CTGGGGACCAAGGTGGACGCAGAGCGCGATGGCTTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCTCCGGCGCCCGACGAGGGCTC
+SRR1177965.5 5 length=101
?7@DD:DD?:<A;<<<:ACA:@C@?:@)7?D;B)(-=FCCHI>C?>EDDB7ABA?5;?8;,9ACCA@BBBBC:?C?<<++(2<95><BB############

==> SRR1177965_R2.fastq <==
@SRR1177965.1 1 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNTNNNNNNNNNNNNNNNN
+SRR1177965.1 1 length=101
#####################################################################################################
@SRR1177965.2 2 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNTNNNNNNNNNNNNNNNN
+SRR1177965.2 2 length=101
#####################################################################################################
@SRR1177965.3 3 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGNNNNCNNNNNNNNNNNNNNNN
+SRR1177965.3 3 length=101
#####################################################################################################
@SRR1177965.4 4 length=101
CCAGGGNNNNNNNNNNNNNNNGANGTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATGGGGACNNNNGCNGNNTNN
+SRR1177965.4 4 length=101
=@###################################################################################################
@SRR1177965.5 5 length=101
CATCCCCAANGCAGCTGTCGGCCTCCTCCACTTCNNNNNNNNNNNNNNAGTNGTCTNNNNNNNNNNNNNNNCCCTCGTCCGTTTCCGGTGCCTTTGGCTTC
+SRR1177965.5 5 length=101
B<BB?DDB?#2<C:;32A?F<8E)?EF?C9HF#####################################################################

Starting FASTQC command


Processing SRR1177965_R1.fastq

Printing command:
fastqc --outdir SRR1177965_R1.fastq

Analysis complete for SRR1177965_R1.fastq

Processing SRR1177965_R2.fastq

Printing command:
fastqc --outdir SRR1177965_R2.fastq

Analysis complete for SRR1177965_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 8.9G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun  9 15:04 .
drwxrwxrwt. 98 root   root       340K Jun  9 15:10 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun  9 15:14 PA_M3_FASTQC
-rw-r--r--   1 kkarri montilab-p 4.5G Jun  9 15:01 SRR1177965_R1.fastq
-rw-r--r--   1 kkarri montilab-p 4.5G Jun  9 15:02 SRR1177965_R2.fastq
==========================================================
Finished on : Fri Jun  9 15:14:07 EDT 2017
0 hours, 12 minutes and 50 seconds elapsed.
==========================================================