-----------------------
Start of variable list:
-----------------------
Sample_ID:
PA_M2
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 15:01:21 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC
Current job ID : 9244394
Current job name : Step_02_PA_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9244394.1.linga

Loading required modules...


List files in scratch directory:

total 3.6G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun  9 15:02 .
drwxrwxrwt. 85 root   root       164K Jun  9 15:01 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun  9 15:02 PA_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 1.8G Jun  9 15:01 SRR1177964_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.8G Jun  9 15:02 SRR1177964_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177964_R1.fastq <==
@SRR1177964.1 1 length=101
CGGCGGGAGAGGTGCGGGCTAAGGGAGACAGAGCCTGGCGCTGAGGAAGGAATCTGGGAGTCGAGAGCTGACTCCAGCCGACGGAACCCGCAGCCCTTGCC
+SRR1177964.1 1 length=101
???DDDDD6DBDB@<D6:;A#################################################################################
@SRR1177964.2 2 length=101
CTAAAATCCTTCCATACAATTAAGTATCAGCGATGTACCATATTGCAGAAAGGGGTGGCTGAGCAACAGTTTGTTGATACTATAAGACTTCCATGCTCAAC
+SRR1177964.2 2 length=101
@@@DDFDFHHHFHIHGBHIHGEGE4CEHGIHIEHIJGIJJIJJJJIGHHIHGIIB7AHIJJBH>EHGFFEEFFEEECEEDDCDACCCDDDDDCDDD@@:C9
@SRR1177964.3 3 length=101
GTGGATGTTCAAGTGATCCATAAAACTCTGCTGCCACAGGCTTCAGGTTGTTGGGAGTCAGGCCTGCATCGTACACCCAACCCCCATCCAAGGTAATGGCA
+SRR1177964.3 3 length=101
@@@DDFFDFHHGHBHGIIG@,A<@FDHCHHGHIJGCHGHGIJI><F>9FBDF;FFCGCGHDAGGEGG>CA=CEFFFFBCDBDB@@BCD9>:>?::A>:A?9
@SRR1177964.4 4 length=101
CTCGCCTCGGCCGGCGCCTAGCAGCCGACTTAGAACTGGTGCGGACCAGGGGAATCCGACTGTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCGGGG
+SRR1177964.4 4 length=101
?@;?DD@DCDBFH6?@GHBGBFCEGG<EGGHIGHHHDHH?CD<>@BBBBB??BBBCCBCCBBCCACCCCCCC@ABBB9(9::5<>BBB>AA?><9<B0930
@SRR1177964.5 5 length=101
TTCTGCCACACCCAGAGTCCACTAACTGGACAGATTACCATGAAATTTCATTAAAATAAAATGTGGATTTAATTTATGAATGGCATTATGATGTTTGTGTA
+SRR1177964.5 5 length=101
@BBFDDDFGHHHHJCFHBHFEHIHJJIJJIIJJJJJJJJIIJJJJIIJJIFIJJHIIJJJIJIGGFGGHGGIIIJJHHFHCEFFFFFFDEDEECCDD=ACC

==> SRR1177964_R2.fastq <==
@SRR1177964.1 1 length=101
TGCAGGCTCTGCTGATTGCTCTGCGCTTCGCTATCNNNNNNNNNNNCCCGTCGCGCTGCTNNNNNNNNNAAGGGCTGCAGGTTCCGTCGGCTGGAGTCAGC
+SRR1177964.1 1 length=101
=?+4B?1+ADFBF:EFH>CHCHAA)@:?<0CDH####################################################################
@SRR1177964.2 2 length=101
GTCTTTGCTCATGAGCTCCCTGCTAGCTTTGCAGTNNNNNNNNTGTACTAGCTTCGATTCTNNNNNNNNTTGTCATGTTGGAAGACAGAAATGTCAGACTT
+SRR1177964.2 2 length=101
@??DDFFDFFHDHIIJJJJJJGGEHIJJJJIJIJ@########0008FIGGIIJIJIGIEF########-,5?BFFECDE?CADBCDDCDCCC@AACCDD@
@SRR1177964.3 3 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SRR1177964.3 3 length=101
#####################################################################################################
@SRR1177964.4 4 length=101
CGCGCTTCATTGAATTTCTTCACTTTGACATTCANNNNNNNNNNNNNNAATCACATCGCNNNNNNNNNNNCCGCGGGCCTTCGCGATGCTTTGTTTTAATT
+SRR1177964.4 4 length=101
B;?DFDADFFDFDHIHIGIIIEDHGH<CHHGGE>##############007BBCEH>;@###########,,5=?@89@BCC?@9>@B<@4@CCC?CA###
@SRR1177964.5 5 length=101
TCCTCAAGCAAGGATCTATCAAAGAAATCCAATCNNNNNNNNNNNNTTATGGGAAGAAGANNNNNNNNNTCTAGGTTGGCTATGTAAATGAGAATCATTTC
+SRR1177964.5 5 length=101
B@;DDDEDGHHHHEHIIGIJJIJJJIGIIIIJHI############00?FEHICHIGHGH#########,,;ADAC@CDDDDDDEEEEEEDDDDCDDCCDE

Starting FASTQC command


Processing SRR1177964_R1.fastq

Printing command:
fastqc --outdir SRR1177964_R1.fastq

Analysis complete for SRR1177964_R1.fastq

Processing SRR1177964_R2.fastq

Printing command:
fastqc --outdir SRR1177964_R2.fastq

Analysis complete for SRR1177964_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 15:05 .
drwxrwxrwt. 82 root   root       164K Jun  9 15:14 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun  9 15:14 PA_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 5.2G Jun  9 15:01 SRR1177964_R1.fastq
-rw-r--r--   1 kkarri montilab-p 5.2G Jun  9 15:02 SRR1177964_R2.fastq
==========================================================
Finished on : Fri Jun  9 15:14:41 EDT 2017
0 hours, 13 minutes and 20 seconds elapsed.
==========================================================