-----------------------
Start of variable list:
-----------------------
Sample_ID:
C_IP6
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 17:15:47 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/02_FASTQC
Current job ID : 9321124
Current job name : Step_02_C_IP6
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9321124.1.linga

Loading required modules...


List files in scratch directory:

total 3.6G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 14 17:16 .
drwxrwxrwt. 57 root   root       164K Jun 14 17:16 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 14 17:16 C_IP6_FASTQC
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 14 17:16 SRR1178004_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 14 17:16 SRR1178004_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1178004_R1.fastq <==
@SRR1178004.1 V0112_0155:5:1101:1033:2052 length=101
NTCCTTGAATCCACAACCCAGACCAAGGCCCAGAGGCTCTTCGATGCGAACAAGGCTGAGCTCTTCACGCAGAGCTGTGCAGACCTCGACAAATGGCTGAN
+SRR1178004.1 V0112_0155:5:1101:1033:2052 length=101
%1:BBDDD??AFCCEHD?@G3CGHGIHGIIGI==F??BGHBD9@DFFHI@8BHFBH:;@D@DC@AA@>?;9??BC%%%%%%%%%%%%%%%%%%%%%%%%%%
@SRR1178004.2 V0112_0155:5:1101:1153:2164 length=101
CCAGCTCTTTAGGCCTGAAGCAGGAGGATGGAGGTTCAAGGCCTGCTTGGGTACATAGCAAGCTCCGCCTTACTCTTACTGATCCCCTGAAAACAACAACC
+SRR1178004.2 V0112_0155:5:1101:1153:2164 length=101
@@@FFFFFHHFHGIIIIEHIHGIIFIIDIIICGEEHH@G>@CBHG@D>9CCFAF7@:CFGB9@GHE<:?BD));>AA@@@5;>;>C15),:CCDB%%%%%%
@SRR1178004.3 V0112_0155:5:1101:1101:2175 length=101
CCCTAACCTAAAAAAACAGATACCCATAGACATACAAGAAGCCTACAGAACTCCAAATAGATTGGACCAGAAAAGAAACACCTCCCGTCACATAATTGTCA
+SRR1178004.3 V0112_0155:5:1101:1101:2175 length=101
CC@FFFFFGHHHHGIIIIFIIIIIIIIIIIIIIIIIIIIIIIGGEIIHIGGGGGEGEHIIGEHEEEEBDFFE@@>?BC??B73<A@=A@@BCCDCC>44>:
@SRR1178004.4 V0112_0155:5:1101:1474:2008 length=101
CTTTTTTACAGACTCTCTCAAGTCTATTACCAATTGGATACAATCTGAGAGTTTCATTCAACACCATATCCAGGTATTCCATTTACATCACAATATCGTAG
+SRR1178004.4 V0112_0155:5:1101:1474:2008 length=101
8?@A?DDAD<AF>CBAC<F3AC9<FBHGIGIIEIEH>?G>@9B<DBBF<FH<<BFDHH:C4B3;F=4;@7@DEHE3?AEH*;;3*7*7>;>3>C5@@1?;8
@SRR1178004.5 V0112_0155:5:1101:1259:2042 length=101
CTATTGTCCAATATATACAAAGAATTCAAGAAGTTAGATTCCAGAGAATCAAATAACTTTATCAAAAATAGGTTATAGAGCTAAACAAAGAGTTCTCAACA
+SRR1178004.5 V0112_0155:5:1101:1259:2042 length=101
@CCFFFFFHGHHGGIIIIIIIGGGIIHIIIIFIIGIIIGIIGIHGIGEIIF<BGIHHGIEEGGEHII?DBFEAAHIIIIIBD3=*.7??>77>6@@@CDC5

==> SRR1178004_R2.fastq <==
@SRR1178004.1 V0112_0155:5:1101:1033:2052 length=101
CACTGGTGAGGTCTTTGCCATAGTCGTCAGATTGAATCTGGCTCTCCAGGCCATGCAGCCATTTGTCGAGGTCTGCACAGCTCTGCGTGAAGAGCTCAGCT
+SRR1178004.1 V0112_0155:5:1101:1033:2052 length=101
?@@D;D2=C?CC?GHIFBGGGI@AEF2AFFB?C9DHEGG<BDGHCIII>GDEGGGIIIIGGEHIIGA<C((5?;CDD@C@=@;@;AB(,8<:>A?CACA%%
@SRR1178004.2 V0112_0155:5:1101:1153:2164 length=101
GCTGGGGGTTGTTTGTTGTTTTCAGGGGATCAGTAAGAGTAAGGCGGAGCTTGCTATGTACCCAAGCAGGCCTTGAACCTCCATCCTCCTGCTTCAGGCCT
+SRR1178004.2 V0112_0155:5:1101:1153:2164 length=101
BCCFFFFF?DHHHDHGIGGIIIC<DHIIHIIIIIIIHGIBFHIIGGHBCCBDADDDDCCDFCCDDBBDDDDB@CDCCCDCDDCDDBCCC?:@CCDC>:<?3
@SRR1178004.3 V0112_0155:5:1101:1101:2175 length=101
CAGTAACCTGGGCTGGCATTTGTGTTCTCTTATGGTCTGTATAACATCAGTCCAGGATCTTCTGGCCTTCATAGTTTCTGGCGAGAAGTCTGGTGTGATTC
+SRR1178004.3 V0112_0155:5:1101:1101:2175 length=101
CCCDFFFFHHHHHIIIIHIIIIFGGHGIIIIIIIIIIGIHIIIIIIHIIFHHIIIIIIIIIIIIIIIIIIIIIIHIFHHFGHFA>>/;>>>AC595<CA@%
@SRR1178004.4 V0112_0155:5:1101:1474:2008 length=101
CCCTGATATTCAGAAGAAACTGCAGGAGGAGATCGATGGGGCCCTGCCGAGTAAGGCACCTCCTACCTACGATATTGTGATGGAAATGGAATACCTGGATA
+SRR1178004.4 V0112_0155:5:1101:1474:2008 length=101
8=B;DDB<D?C<4:CEG?CG:3AABF222:BC?:1*C90*??FG?DG@AAA5=@D@>2=;;BB37@A@:;9(;)8@3)53;5>?@@>:@@C%%%%%%%%%%
@SRR1178004.5 V0112_0155:5:1101:1259:2042 length=101
CCAACAATGAAGGAGTGTTTCTCTTTCTCCACATCCTCGCCAGCATCTGCTGTCACCTAAGTTTTGATCTTAGCCATTCTGAGGGGTGTGAGGTAAAATCT
+SRR1178004.5 V0112_0155:5:1101:1259:2042 length=101
CCCFFFFFHHHHHGICGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHGIIIIHHGCHFFDFFEEF;@BDBBB=BACD>CCADEC3

Starting FASTQC command


Processing SRR1178004_R1.fastq

Printing command:
fastqc --outdir SRR1178004_R1.fastq

Analysis complete for SRR1178004_R1.fastq

Processing SRR1178004_R2.fastq

Printing command:
fastqc --outdir SRR1178004_R2.fastq

Analysis complete for SRR1178004_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 12G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 14 17:25 .
drwxrwxrwt. 52 root   root       164K Jun 14 17:31 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 14 17:33 C_IP6_FASTQC
-rw-r--r--   1 kkarri montilab-p 6.0G Jun 14 17:16 SRR1178004_R1.fastq
-rw-r--r--   1 kkarri montilab-p 6.0G Jun 14 17:16 SRR1178004_R2.fastq
==========================================================
Finished on : Wed Jun 14 17:33:33 EDT 2017
0 hours, 17 minutes and 46 seconds elapsed.
==========================================================