-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M5
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-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/02_FASTQC
Current job ID : 6936715
Current job name : Step_02_G167_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936715.1.linga

Loading required modules...


List files in scratch directory:

total 2.5G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:56 .
drwxrwxrwt. 81 root   root      112K Jul 14 19:56 ..
-rwxr-xr-x   1 kkarri waxmanlab 1.3G Jul 14 19:56 5_S27_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.3G Jul 14 19:56 5_S27_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:56 G167_M5_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 5_S27_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1996:1226 1:N:0:ATCCACTG+ACGCACCT
AGCGATCTTAATGGCTTCTTCAACATATGGGAATGTGAGGAAGGAGTAAGGCAAACCAAGGTGATACACAAGACGGCCACATCTGTCATAGATGAGGAAGTCATCTTTGTTTCCATTTAAGAGAGTCCAGACATCTATGCCATCTTCTTCT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJFJJJJ7<JJFJJAFFJFFAFFFJJJJFJJJJJFJJFFFJJJJ
@J00170:103:HMYG2BBXX:4:1101:3802:1226 1:N:0:ATCCACTG+ACGCACCT
ATTCGCTTTACCGGATAAAACTGCGTACGTCGGGAGCGAGAGCGCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATTAGTCTTTCGCCCCTATACCCAGGTCGGACGACCGATTTGCACGTCAGGACCGCT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJFJJJ
@J00170:103:HMYG2BBXX:4:1101:3924:1226 1:N:0:ATCCACTG+ACGCACCT
CAGGAATGGAAAAAGTACTACTGAGAAGAGCAAAGGATCAAAAAAATCAAATCTTAAAAGCTTTTTGGCTTTCTCCACAAAAGGATCCTCTGGGTTGTTGAGGGAATCCACGTTCACTCCAAATGATGTGCTGGTGATCAAGATCGGAAGA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJFJJJAFAFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJ<F-FJJJFJJJFJJJJA
@J00170:103:HMYG2BBXX:4:1101:4777:1226 1:N:0:ATCCACTG+ACGCACCT
CTCATTTGTTCTTGGCTGCTAGGGGTTTCCGGCTGATCTTTTTTGATTTGTCGTTATTCTTCTTTGGAGGTTCTGGGTTCGCTTGCATGTGTCTGCCGTAGAGGTACTTGTAAGTTTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJFJJJJJJJJJJJJJJJJJJFFJFJJJFJJFJJ-FJJJJJFFFJJFFJFJJF<FFJJFFFFJFFJJFF<FFA
@J00170:103:HMYG2BBXX:4:1101:5365:1226 1:N:0:ATCCACTG+ACGCACCT
CTGAGCCTTGGTGTCTTCTCCCACCACGCGCAGCTGCTCCTGCAGCTCCTGCACACTCAGGCCCACCTGCTCCATCAGCTCCGCCGTGTAGGGTTTCAACTGCTGCCTCAGGCCCTCCAAGTTCCAGCCTACCTGCTGGTGCTTCGCAGCC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJFJJJFJFAJFJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

==> 5_S27_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1996:1226 2:N:0:ATCCACTG+ACGCACCT
AACACATCGCAGTGTACAGACAAGAAGAAGATGGCATAGATGTCTGGACTCTCTTAAATGGAAACAAAGATGACTTCCTCATCTATGACAGATGTGGCCGTCTTGTGTATCACCTTGGTTTGCCTTACTCCTTCCTCACATTCCCATATGT
+
AAFFFJJJJJJJ7FJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJFJJAJJJJFJJJFJFJJJFFJJJJJJJJJFJJJJJJJJJAJJJJJJJJJJJJFAJJJJAJJJJJJFFJJFJJJ
@J00170:103:HMYG2BBXX:4:1101:3802:1226 2:N:0:ATCCACTG+ACGCACCT
CTCTGGTGGAGGTNCGTAGCGGTCCTGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCTCCCGACGTACGCAGTTT
+
AAFFFJFJJJJJF#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJJFFJJJFJJJJJJJJ<FFFJJJJFJJJJJFJJJAJJJJJJJJJJJJJFAJJ
@J00170:103:HMYG2BBXX:4:1101:3924:1226 2:N:0:ATCCACTG+ACGCACCT
TGATCACCAGCACNTCATTTGGAGTGAACGTGGATTCCCTCAACAACCCAGAGGATCCTTTTGTGGAGAAAGCCAAAAAGCTTTTAAGATTTGATTTTTTTGATCCTTTGCTCTTCTCAGTAGTACTTTTTCCATTCCTGAGATCGGAAGA
+
AAFFFJJJJJJJJ#JJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJFJJJJJJJJJFJFJJJJJJJJJJJJJJFJJFJFFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFFFFJJF<-7<F<AFFJ
@J00170:103:HMYG2BBXX:4:1101:4777:1226 2:N:0:ATCCACTG+ACGCACCT
CAGAAACTTACAANTACCTCTACGGCAGACACATGCAAGCGAACCCAGAACCTCCAAAGAAGAATAACGACAAATCAAAAAAGATCAGCCGGAAACCCCTAGCAGCCAAGAACAAATGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGT
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJAJJAJ<JJJJJJJJJJ-
@J00170:103:HMYG2BBXX:4:1101:5365:1226 2:N:0:ATCCACTG+ACGCACCT
CGGAAACAGCTGCNGCAGGAGCTGGGGGAAGTGAGCTCGCGCCTGGAGCCCTACATGGCTGCGAAGCACCAGCAGGTAGGCTGGAACTTGGAGGGCCTGAGGCAGCAGTTGAAACCCTACACGGCGGAGCTGATGGAGCAGGTGGGCCTGA
+
AAAFFFJJJJJJJ#JJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJAFJJJFJAAFJJJJ-<7

Starting FASTQC command


Processing 5_S27_R1_001.fastq

Printing command:
fastqc --outdir 5_S27_R1_001.fastq

Analysis complete for 5_S27_R1_001.fastq

Processing 5_S27_R2_001.fastq

Printing command:
fastqc --outdir 5_S27_R2_001.fastq

Analysis complete for 5_S27_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 19:58 .
drwxrwxrwt. 79 root   root      112K Jul 14 20:05 ..
-rwxr-xr-x   1 kkarri waxmanlab 5.7G Jul 14 19:56 5_S27_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 5.7G Jul 14 19:56 5_S27_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:05 G167_M5_FASTQC
==========================================================
Finished on : Sat Jul 14 20:05:45 EDT 2018
0 hours, 9 minutes and 33 seconds elapsed.
==========================================================