-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M2
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 : 6936712
Current job name : Step_02_G167_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936712.1.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 1.5G Jul 14 19:56 2_S24_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.5G Jul 14 19:57 2_S24_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:57 G167_M2_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 2_S24_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:2463:1226 1:N:0:TTATAACC+TCGATATC
CTAGCTTCTTCTGCATGGACACACACTAGGGTCAGCCCCAAACACAGCAGCAGCAGCATCTTCATTTTGGTAGGGAATAGGATTGTCTGTCTGTCAGGACCACGTCTTTCTTGTGATCGTGAGATCGGAAGAGCACACGTCTGAACTCCAG
+
AAFFFJJJJJJJJJFJFJJJJJJJFJJFJJFFJJJJJJJJJFJJJFJJAFF<JJAJJJAJJFJJFAJJFJJFFJFJJJJJFJJJJJJJJJJJJ<JFJAFJFFJJAJJFJJJJJJJJJJA<FFJJJFFJJJJJJFFFJJJJJJJJFJJJJJF
@J00170:103:HMYG2BBXX:4:1101:2706:1226 1:N:0:TTATAACC+TCGATATC
CAAACAATAAGGAATGTTGATCCAATAATTACATGGAGTCCATGGAATCCAGTAGCCATGAAGAATGTAGAACCATAGATACCATCTGAAATGGAGAATGATGTTTCAAAGTATTCTGAAGCTTGGAGGATGGTGAAGTAAAGTCCTAGTA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJFFJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJFJFFJJJJJJFJFFJFFJJJJAJ-FJJFF
@J00170:103:HMYG2BBXX:4:1101:3965:1226 1:N:0:TTATAACC+TCGATATC
CTTCCTTCACTTCTTCTTTTGGAATCCCTGCCTTCTCAATGGCTCCCTGAATTGCAGCAGTACCAAGTTTAGTGGCCGGCTGAGAGGCAAGGCTGCCCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTATAACCATCTCCTAT
+
AAFFFJJFFJJJFJJJFJJJJFFFJJJJAAJJJJJAJAFA--FAAJJAAJJFJ<F7AF7AFAAJF--FJJJ7JJ-AAA-<F7JFFJFAFJ7J7F<F7JFJAAFJFAJJ7F<JFJJJJF7JA<JJJJJJ-AF<FJFJ7FJJJJJ<F<J-A7<
@J00170:103:HMYG2BBXX:4:1101:4148:1226 1:N:0:TTATAACC+TCGATATC
CAACCAGCTTTGAGGCAGGGATCCCAGATGCTCTCTCAAGCCCGTCGATGTTCTGTGTATAGAGCCGCAGAAGCAGCTCCTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTATAACCATCTCGTATGCCGTCTTCTGCTT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ77FJJJJJJJJF7FA7FJJJJJ
@J00170:103:HMYG2BBXX:4:1101:4290:1226 1:N:0:TTATAACC+TCGATATC
GGGAGATCTAAATACTGCCACAGTCTAACTTCACAGTATTCTAAAAAGGCTTACTAAAAATATTCAGCAAATTTTAACAGCTACTGATTTACTGACTGCTACTATATGCTAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAT
+
AAFAFFJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJFJJJJJJJJJJJJFJJJJAJJJJJJJJJJJJJJJJAJJJJJJJFJJFJJJJJJJJJJFJJJJJJJ7AJJJJJJJJJJJJJJJJJFJJJJJJJ<<FFFFJJJJFAFJJJJJJJJJ

==> 2_S24_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:2463:1226 2:N:0:TTATAACC+TCGATATC
CACGATCACAAGANAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGGCTGACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAG
+
AAF<AFFAAAJFJ#JJJJJFJJJJF<JJFFFFJJFJJJJFJJFJJFJFFJJFJJJAJFJFJFFFJJJAF<<<7FJFAAFJF<7JFJJJJFJJ7FAJAA-7AF-A<A--7FJFFFJJAFF<-<7FAAFFFJF<-<AFA<AA--<FJFJ<---
@J00170:103:HMYG2BBXX:4:1101:2706:1226 2:N:0:TTATAACC+TCGATATC
CATTATACTAGGANTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGATTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATT
+
AA<FFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJAAJJJJJJFJJJJJJJJJJJFJJJ<<JJJJJJJFJJJJJJFJJJJJFJJJJJJFJFJ-<<AFFJJF77AJFFJ7A
@J00170:103:HMYG2BBXX:4:1101:3965:1226 2:N:0:TTATAACC+TCGATATC
CTGGGCAGCCTTGNCTCTCAGCCGGCCACTAAACTTGGTACTGCTGCAATTCAGGGAGCCATTGAGAAGGCAGGGATTCCAAAAGAAGAAGTGAAGGAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGATATCGTGTAGATCT
+
AAFAFJJJJJJJJ#JFJJJJJJJJJJJJJJJJJJFJJJFJJJFJFJJJFAJJJJJFJJJJJFAAJJJJFJJFFJJJFJJJJJJJJJJJJJJ<AJFFFJJF7FJ<JJJJJJJJJ<A<<FJFFFJJJJJJJJFFJJJJJJJJ<F<JJFJAFJ-
@J00170:103:HMYG2BBXX:4:1101:4148:1226 2:N:0:TTATAACC+TCGATATC
CGACAAGGAGCTGNTTCTGCGGCTCTATACACAGAACATCGACGGGCTTGAGAGAGCATCTGGGATCCCTGCCTCAAAGCTGGTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGATATCGTGTAGATCTCGGTGGTCGCCGTA
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJFJJJJJFJFJJFJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJFJ
@J00170:103:HMYG2BBXX:4:1101:4290:1226 2:N:0:TTATAACC+TCGATATC
TTTAGCATATAGTNGCAGTCAGTAAATCAGTAGCTGTTAAAATTTGCTGAATATTTTTAGTAAGCCTTTTTAGAATACTGTGAAGTTAGACTGTGGCAGTATTTAGATCTCCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGAT
+
AAFFFJJJJJJJJ#JJJJFJJFJJJJJJJJJJJJFJJJJJJJFJFFJFJJJJJJJJJFJJJJJJJJF<FJJJJJJJJJJJJJJJJJJJ-<JJ77FAJF<JFJFJF<FFF-FJJJJJJJJJJJJJJFF7AFJJJF7FFFF<AA<-<7FF<F7

Starting FASTQC command


Processing 2_S24_R1_001.fastq

Printing command:
fastqc --outdir 2_S24_R1_001.fastq

Analysis complete for 2_S24_R1_001.fastq

Processing 2_S24_R2_001.fastq

Printing command:
fastqc --outdir 2_S24_R2_001.fastq

Analysis complete for 2_S24_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 12G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 20:00 .
drwxrwxrwt. 68 root   root      268K Jul 14 20:06 ..
-rwxr-xr-x   1 kkarri waxmanlab 6.0G Jul 14 19:56 2_S24_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 6.0G Jul 14 19:57 2_S24_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:08 G167_M2_FASTQC
==========================================================
Finished on : Sat Jul 14 20:08:08 EDT 2018
0 hours, 11 minutes and 56 seconds elapsed.
==========================================================