-----------------------
Start of variable list:
-----------------------
Sample_ID:
AB1_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 15:01:17 EDT 2017
Running on node : scc-ka7
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/02_FASTQC
Current job ID : 9244383
Current job name : Step_02_AB1_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9244383.1.linga

Loading required modules...


List files in scratch directory:

total 3.3G
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 AB1_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 1.7G Jun  9 15:01 SRR1177979_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.7G Jun  9 15:02 SRR1177979_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177979_R1.fastq <==
@SRR1177979.1 1 length=101
CCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGATGGTTGTGATGTGTTTAGGCTAAGGCTTCTTTGCTTCTAGCAACAAGGTTTGGCCCCTCAG
+SRR1177979.1 1 length=101
??8BADADDBDBDE<E>E:CFIDD4EEEEDDD;DDDDDDE><DDDDD7=)8BC)8@A>CCCDEID>AC>ADD>?AAA6>;@AA>????:>>??AA??>52>
@SRR1177979.2 2 length=101
GCGAGGCATACCTGGTGGGGTTGTTTGAAGATACCAATCTGTGTGCCATCCACGCCAAGAGAGTCACCATCATGCCCAAAGACATCCAGTTGGCTCGCCGG
+SRR1177979.2 2 length=101
???DDDDDDDDDDII:CEEE:D@DDIIDE9DDA?BDCDIIECEB9@CAD>A@7;<=@D@A@@@>AAA>AA;>AAAA?A???A?AAAAAAAAA>>A>>>;>;
@SRR1177979.3 3 length=101
GAAAAGTTTGCAAAACTATGTGAGGCGCATGGAATCACTAGGGACAATATCATTGATCTAACCAAGACTTATCGCTGTCTCCATGCCCGAGGATGAAGAAA
+SRR1177979.3 3 length=101
=??DDDD,22=B?D;EDE?CA,:EECEE?DDD@3?@<DDD?DDDIDC8BB)8AC:78AACAA>CDCC;C))7?.5><3;AAAA(5:>?;8?59AA:AAAA9
@SRR1177979.4 4 length=101
CATCTCAAAGGTCTTTTCTGTAGCTTTGTATAGCTTTTCATTCAATCCTAATTAAGTTCCTTTACTGATCTAGAAAATGTAACCAGAATATTCTTCTCATT
+SRR1177979.4 4 length=101
??1+A=BD>+A:A?ABAEEI>EDCF@@<CFEAF4AF?CEEBE@91?CDAB00?B<9B9?DDEEEIED8BBE<BC)8@AC=@AEC;26?))777?>@3?@DD
@SRR1177979.5 5 length=101
TCCAGGTAAGAAACGACCGGTGTAGTTGATCTTCTCCACCAGGGTGTGCGTGGTATCTCCATACGTCTGCAGCACAGCGAACTTCACCTTCCCGAATTTGT
+SRR1177979.5 5 length=101
@@@DBEBDHDFFHIIIIIIIED8DH?FDHIIIIIIIIBHHIIIGBDGIBBEAE6=@DFFFFFEEE@ACDDDCCDDDCDDBBDDDDCCDDCCCDDD&<ACCA

==> SRR1177979_R2.fastq <==
@SRR1177979.1 1 length=101
CTGAAGACGGTGATGGGTGACTTCGCACAATTCGTGNACAAGTGTTGCAAGGCTGCCGACAANNNNAACTGCTTCGCCACTGAGGGGCCAAACCTTGTTGC
+SRR1177979.1 1 length=101
BB@DBDBD@?FBDHF<FF8ACFGIIBGGFIDBFDDG#0)?FE/908B<FGC;=CEHGF84==####,,5,8:@::=?DDDDCCCB7>BD@BD(<ACDDC24
@SRR1177979.2 2 length=101
CTTCAACTTAAGCTCTCTCCCCCCGTATCCGGCGAGCCAACTGGATGTCTTTGGGCATGATGGTGACTCTCTTGGCGTGGATGGCACACAGATTGGTATCT
+SRR1177979.2 2 length=101
@;;BDFED8DBHABGFAHCGGFFGF:CDHC?6DGGHIHEHFFDE>AC.6@C@ACBBCD@CDDD>ACCDCCCCCAAC<9<B?CA?<?CC?BB?CC>?3:@C>
@SRR1177979.3 3 length=101
CTGGTGAGNNNGCTCCACTCAGCACTGGAGGCTNNNNNNNNNNNNNNNNNNCNNGCNNNNNNNNNNNNNNNAGTCTTTGTTAGATCAATNATATTGTCCCT
+SRR1177979.3 3 length=101
=@=+=A=D###+22A<EAFAAEFHAH;1:?)??####################################################################
@SRR1177979.4 4 length=101
CGGGGTAAAATAAATTCCTTTAACGTTGATCTACTAATGAGAAGAATATTCTGTTTACATTTNNNNGATCAGTAAAGGAACTTAATTAGGATTTAATGAAA
+SRR1177979.4 4 length=101
;?@;:D6B4D4FCBC:+<::AAFHG2<ABB**1C4EBFCBH*?F@?<?9BB<**09EGF@A@#######################################
@SRR1177979.5 5 length=101
NNNNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACANCGGNNNNNNNNNNNNNNN
+SRR1177979.5 5 length=101
#####################################################################################################

Starting FASTQC command


Processing SRR1177979_R1.fastq

Printing command:
fastqc --outdir SRR1177979_R1.fastq

Analysis complete for SRR1177979_R1.fastq

Processing SRR1177979_R2.fastq

Printing command:
fastqc --outdir SRR1177979_R2.fastq

Analysis complete for SRR1177979_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.4G
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 AB1_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 4.7G Jun  9 15:01 SRR1177979_R1.fastq
-rw-r--r--   1 kkarri montilab-p 4.7G Jun  9 15:02 SRR1177979_R2.fastq
==========================================================
Finished on : Fri Jun  9 15:14:11 EDT 2017
0 hours, 12 minutes and 54 seconds elapsed.
==========================================================