-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M7
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G167
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jul 14 19:56:12 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/02_FASTQC
Current job ID : 6936717
Current job name : Step_02_G167_M7
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936717.1.linga

Loading required modules...


List files in scratch directory:

total 2.9G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:57 .
drwxrwxrwt. 71 root   root      268K Jul 14 19:56 ..
-rwxr-xr-x   1 kkarri waxmanlab 1.4G Jul 14 19:56 7_S29_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.5G Jul 14 19:57 7_S29_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:57 G167_M7_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 7_S29_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1955:1226 1:N:0:CAAGCTAG+CGCTATGT
TGGTCATGTAGTCCCGCATGGTCTCGTAGATTGCGAACCGAGTCAGAGAGTAGGTCATCTGCCTGCACAGCGAGGCACTCAGGCCGTTGTAGAGCGCCAGGAAGCCATCGGTTCGCACCACCTGCAGTGCCATTCCAGTCATGCGCAGCTT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJAFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJFJFFJJJJJJFJJJFAFJAAJFJFAFFJ
@J00170:103:HMYG2BBXX:4:1101:1976:1226 1:N:0:CAAGCTAG+CGCTATGT
GTGGACACTCCAGCATCTCTGAGGCTACGGGACAAGAGCACAGCCGGGATACCAAAAAATATATCTCCAAACATGTCCAGGATAAGCTCACTCTTTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGCTAGATCTCGTATGC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJFFFJFJJJ<F
@J00170:103:HMYG2BBXX:4:1101:2849:1226 1:N:0:CAAGCTAG+CGCTATGT
CCAAAGTGTTCCTGTGCCACTTTGAGAATCTCCCAGATCAAGTCTTCCTTGCCATTGTTTTTTCGAGCCACAACAGCATGAGAAGGGATCCGAGCCAGGTAGCAATCCTCATACTGATCCACTGGCTTGCGGAGATCGGAAGAGCACACGT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJFFFJJJJJJJJJFJJJJF
@J00170:103:HMYG2BBXX:4:1101:3072:1226 1:N:0:CAAGCTAG+CGCTATGT
GAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTTTTGTCAGAGGCCAGGATAATAGTATGCCATTCCCCATTAATCTTTTGTACATTAAAGTTCCTTCCCGTAGAACTAGCTTCTTCAGATCGGAAGAGCACACGTCTGAACTC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJFAAJJJJJJJJJFJJ<FFJJJJ
@J00170:103:HMYG2BBXX:4:1101:3417:1226 1:N:0:CAAGCTAG+CGCTATGT
AATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGCTAGATCTCGTATGCCG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJFFJJFFJJJJJJJJJJFFJJJJJJJJJJFFFJJJJJFJJJAJF<FJFJJJJJJJ

==> 7_S29_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1955:1226 2:N:0:CAAGCTAG+CGCTATGT
CTGGCTTCCTGCGGAGCCGCTTGCTGCACGCACCCGCTGGACCTGCTCAAGGTGCATCTACAGACCCAACAGGAGGTGAAGCTGCGCATGACTGGAATGGCACTGCAGGTGGTGCGAACCGATGGCTTCCTGGCGCTCTACAACGGCCTGA
+
AAAFFAFJJJFJAFJJJJJJJJJJFAJJJJJJJJJJJFJFF<JJJJAJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJ<JJFFFFJFAJFJJJJJJJJFAJJJJJJJJJJJFF7J<FFAAAJJAJ7<<FFJFJJFJFFJJ
@J00170:103:HMYG2BBXX:4:1101:1976:1226 2:N:0:CAAGCTAG+CGCTATGT
AAAAAGAGTGAGCTTATCCTGGACATGTTTGGAGATATATTTTTTGGTATCCCGGCTGTGCTCTTGTCCCGTAGCCTCAGAGATGCTGGAGTGTCCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGCTATGTGTGTAGATCTCG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJ7JFFJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJFFJ<A7FJJJJJJFJJJJJFFJJJFJFAJFJFFJJJJJJJ<7<FFJ-FAFFJJJ7FFFJJFJA
@J00170:103:HMYG2BBXX:4:1101:2849:1226 2:N:0:CAAGCTAG+CGCTATGT
CCGCAAGCCAGTGNATCAGTATGAGGATTGCTACCTGGCTCGGATCCCTTCTCATGCTGTTGTGGCTCGAAAAAACAATGGCAAGGAAGACTTGATCTGGGAGATTCTCAAAGTGGCACAGGAACACTTTGGAGATCGGAAGAGCGTCGTG
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJ-FFJFJJJJJFJJJJJJJJAJJJJJJFJJFJJJJJJJJJJJJFFJJJJJJJJJJJFAFJJ<FA7FFFFFJJFA
@J00170:103:HMYG2BBXX:4:1101:3072:1226 2:N:0:CAAGCTAG+CGCTATGT
GAAGAAGCTAGTTNTACGGGAAGGAACTTTAATGTACAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCAGATCGGAAGAGCGTCGTGTAGGGAAA
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJFJFJJJJJJJ
@J00170:103:HMYG2BBXX:4:1101:3417:1226 2:N:0:CAAGCTAG+CGCTATGT
CGCAGCTAGGAATNATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGCTATGTGTGTAGATCTCGGG
+
AAFFFJJJJFJJJ#FJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJJFJJAJJJJJJJJFJJJJFAFJJJJJJJJJJJJ7FJFJJ<J<AFAJJJJAJJJFAFA)

Starting FASTQC command


Processing 7_S29_R1_001.fastq

Printing command:
fastqc --outdir 7_S29_R1_001.fastq

Analysis complete for 7_S29_R1_001.fastq

Processing 7_S29_R2_001.fastq

Printing command:
fastqc --outdir 7_S29_R2_001.fastq

Analysis complete for 7_S29_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 13G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 20:00 .
drwxrwxrwt. 67 root   root      268K Jul 14 20:08 ..
-rwxr-xr-x   1 kkarri waxmanlab 6.4G Jul 14 19:56 7_S29_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 6.4G Jul 14 19:57 7_S29_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:08 G167_M7_FASTQC
==========================================================
Finished on : Sat Jul 14 20:08:37 EDT 2018
0 hours, 12 minutes and 25 seconds elapsed.
==========================================================