-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M1
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 : 6936711
Current job name : Step_02_G167_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936711.1.linga

Loading required modules...


List files in scratch directory:

total 3.2G
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 1.6G Jul 14 19:57 1_S23_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.7G Jul 14 19:57 1_S23_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:57 G167_M1_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 1_S23_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1407:1226 1:N:0:CCGCGGTT+CTAGCGCT
CACAATCACGACATGTGGACTAACCCAGGAGAGGGCACAGGGACACTGGGCAGGGCTGGCACCTAGTCCTCCTCACCCGGGTCCTCTCTCTCCAGAGTGTAGACCATGAAGCAAGCGTCGGGTCTCTTGGGGACAAGGGGATGCCCGGGTC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJFFJJJJJJ77
@J00170:103:HMYG2BBXX:4:1101:1489:1226 1:N:0:CCGCGGTT+CTAGCGCT
TGCATACCTGCCTTCACTAAGGGACACAGAAGACTGTTAGAAAAGCCAACTGCTTGGGGCTCTATCTGTAATCACAATCCTCACTGTCTTTGCAAAAATCCCTGGATATCATAGACAGTCCCTAATTTTCTTCCCGGAGGCCCTCTTCCTT
+
AAAFFJJF7JJJ<F<<A-F<JJJJJJJJJFJFAFJFFJJJJFJ<FFJFFF<FJJFJJAJJAA<7-AFAFFFFF7A<<AFJF7FFJJAFAFAJJJ7<AJJJJJFJJJJJFJFAJ-AF<JJ<-AJ-A--AJJAAA-7<7-<A7<7-A<F<F<A
@J00170:103:HMYG2BBXX:4:1101:3275:1226 1:N:0:CCGCGGTT+CTAGCGCT
GAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJJFJJJJJJJJFJJJJJJJJ<
@J00170:103:HMYG2BBXX:4:1101:3762:1226 1:N:0:CCGCGGTT+CTAGCGCT
GCAGACTTTCCTCCTCTCCATCCTTGGCTTCGGATTTCATTGTGAAGGTTTCTGTACGCCTATTGATGTTCCCTCCCGTTAATACTCCTCGCAGCTGGGGCGCTCCCGGGAATCCGGCCCCGTCGGCTCCGAGAGATCGGAAGAGCACACG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<AJJJJJJJJJJJJJJJJJJJFAFJJJJJJJJJJJJJJJJJ
@J00170:103:HMYG2BBXX:4:1101:3904:1226 1:N:0:CCGCGGTT+CTAGCGCT
CCGGGTTCCAGCCCACTTTCCAGGGCCCTGTAGGCGATACTGGACTGGAGTACAGGGCCCCAGTAGTAACCGTAATGCCAGCCTGGGGTCAGTGAAGACCAGAGGCAGGATATTGGGCCTGACAGATCGGAAGAGCACACGTCTGAACTCC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFFJ

==> 1_S23_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1407:1226 2:N:0:CCGCGGTT+CTAGCGCT
TTTTCATCTGCTTCCCCAANAACCGTGAGGACAGAGCCGCCNTACTCCGAACCTTCAGCTTTCTTGGCTTTGAGATTGTGAGACCCGGGCATCCCNTNGTCCCNAAGAGACCCGACGCTTGCTTCATGGTCTACNCTCTGGAGAGAGAGGA
+
AAAFFFJJJJJJJJJJJFJ#JJFF<AJJJJJJJJJJJJAJJ#JJJ7FJAAFJJAJJJJJJFJJFJJJJJJFFJF--77AAAF-AFF777<<A-FA#J#7AFFF#J<77-AJFJJ<FFJ<-FJ-AJFF<FFAFJJ#F--7-77)777---)7
@J00170:103:HMYG2BBXX:4:1101:1489:1226 2:N:0:CCGCGGTT+CTAGCGCT
CTGACAGTTGGGGAATCCCAAGTCCACTGGCCTTTAGAAGAGGGAGATGGGAGGTGAAACAGAAGGAAGAGGGCCTCCGGGAAGAAAATTAGGGACTGTCTATGATATCCAGGGATTTTTGCAAAGACAGTGAGGATTGTGATTACAGATA
+
AAFAFJJJ7<JFF<FJFJJJFFJJJJJJJJJJ--FFAAFJ<JJJFJJFFJAFJ--AFJJFF<A-AFJJJJ--<FF7-7A<F<AAFJFJ-7FAJFFAA--<A7AFJJJ<FFAFJFJF7FFFJFFJA7FA<A<A--<FJ<7F77-AF7AJJFF
@J00170:103:HMYG2BBXX:4:1101:3275:1226 2:N:0:CCGCGGTT+CTAGCGCT
GTTGAGTGGAGACNTCTCACCAGGACTCCACCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCACTGAGAAGTCCAATTCCAGTCTATCCACATGTTACCTAGGATACCTCATCAA
+
AAAFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJ
@J00170:103:HMYG2BBXX:4:1101:3762:1226 2:N:0:CCGCGGTT+CTAGCGCT
CTCGGAGCCGACGNGGCCGGATTCCCGGGAGCGCCCCAGCTGCGAGGAGTATTAACGGGAGGGAACATCAATAGGCGTACAGAAACCTTCACAATGAAATCCGAAGCCAAGGATGGAGAGGAGGAAAGTCTGCAGATCGGAAGAGCGTCGT
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<J-FJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJFAFJJJJJJJJAF<JFAFFFFFJAFJJ)
@J00170:103:HMYG2BBXX:4:1101:3904:1226 2:N:0:CCGCGGTT+CTAGCGCT
GTCAGGCCCAATANCCTGCCTCTGGTCTTCACTGACCCCAGGCTGGCATTACGGTTACTACTGGGGCCCTGTACTCCAGTCCAGTATCGCCTACAGGGCCCTGGAAAGTGGGCTGGAACCCGGAGATCGGAAGAGCGTCGTGTAGGGAAAG
+
AAFFFJJJJJJJJ#JJJJJJJJJJJFJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJAJJFJJJFFAJJJAAJFJJJFJJJJJJJJJJJJJJ-JJ7FJJJJJJJJJFJJJJ<JFJJ<JJF

Starting FASTQC command


Processing 1_S23_R1_001.fastq

Printing command:
fastqc --outdir 1_S23_R1_001.fastq

Analysis complete for 1_S23_R1_001.fastq

Processing 1_S23_R2_001.fastq

Printing command:
fastqc --outdir 1_S23_R2_001.fastq

Analysis complete for 1_S23_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 15G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 20:00 .
drwxrwxrwt. 66 root   root      268K Jul 14 20:08 ..
-rwxr-xr-x   1 kkarri waxmanlab 7.2G Jul 14 19:57 1_S23_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 7.2G Jul 14 19:57 1_S23_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:09 G167_M1_FASTQC
==========================================================
Finished on : Sat Jul 14 20:09:50 EDT 2018
0 hours, 13 minutes and 38 seconds elapsed.
==========================================================