-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M8
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 : 6936718
Current job name : Step_02_G167_M8
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936718.1.linga

Loading required modules...


List files in scratch directory:

total 2.4G
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 1.2G Jul 14 19:56 8_S30_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.3G Jul 14 19:56 8_S30_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:56 G167_M8_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 8_S30_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1874:1226 1:N:0:TGGATCGA+TATCGCAC
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGGATCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAACACAGCCAAGAACTCAGTTATCAGTCGAAGACCCTGCGTTTAATCCGTCAGACGTTTTGCCTACGAGGGGATG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJF<JJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJ7-7<7---7---------7----77--77-7--<-77-----------------77-7------7---7-A----
@J00170:103:HMYG2BBXX:4:1101:3295:1226 1:N:0:TGGATCGA+TATCGCAC
CACTCCAAACTGCATCTCAAACCCATCTTCAGTCTTCGTATACGGGCAGTGGAAAACCCCCGCATTATTGATCAGGACGTCTAGCCTGGGCTCCTCCTGTAGCAGTTCTTGGCAGAAAGCTCGCACTGAGCGCAGCGAGGCAAGGTCCAGC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJFFJFFJJJJJJAJJJFFAAJAJJFJJFFJJJJJFJJJJJJJJ-FFJJF
@J00170:103:HMYG2BBXX:4:1101:3863:1226 1:N:0:TGGATCGA+TATCGCAC
AAAGACCTTAACGGTCACGTAGTGGCAGTGCGCCTCACTTGCGCGAACAAGGTCGACAGAAGTCAAGTTCCACGCCACTTCCTTGCTCTTCCTGTGACTCACTTGGGCCTGAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@J00170:103:HMYG2BBXX:4:1101:4594:1226 1:N:0:TGGATCGA+TATCGCAC
CAGAATCTCATTGTACTGCTCAGCATAGTAAAGAAGTTCTGGGGCATAGAAATAAGGATGTCTTCTGGCAACTTCATGCAAATAGTGTCCCATAAAGGTGGTTGGGTTTTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGGAT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@J00170:103:HMYG2BBXX:4:1101:6055:1226 1:N:0:TGGATCGA+TNTCGCAC
GGCAGCANTAACTTGGCCCCTTCCCTCAGTAGAGCTGACCAGATGGATACACTGCTGTTAGCCAAGACAAGTCCCTACTGAATGTGATGGTCTGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGGATCGAATCTCGTATGCCG
+
AAFFFJF#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<<FJJJJJJJJJ

==> 8_S30_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1874:1226 2:N:0:TGGATCGA+TATCGCAC
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTATCGCACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAGAAGGACAATGACATTTCATATCATAAAAACTAATACTATACCAATTATTAGAAGTATCTCGTAA
+
AAAFFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJAJJJJJJJJJJJA7-7-----7----7-----7-7-----77A----7-7----------7------7------7-7--7-7--
@J00170:103:HMYG2BBXX:4:1101:3295:1226 2:N:0:TGGATCGA+TATCGCAC
CCGATGGCCAGCTNGTCGTTAAGGAGCTGGACCTTGCCTCGCTGCGCTCAGTGCGAGCTTTCTGCCAAGAACTGCTACAGGAGGAGCCCAGGCTAGACGTCCTGATCAATAATGCGGGGGTTTTCCACTGCCCGTATACGAAGACTGAAGA
+
AAAFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJFJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJFJJJJJJ7FJF<FFJF
@J00170:103:HMYG2BBXX:4:1101:3863:1226 2:N:0:TGGATCGA+TATCGCAC
CTTCAGGCCCAAGNGAGTCACAGGAAGAGCAAGGAAGTGGCGTGGAACTTGACTTCTGTCGACCTTGTTCGCGCAAGTGAGGCGCACTGCCACTACGTGACCGTTAAGGTCTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTATC
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJFJJ<JJJ
@J00170:103:HMYG2BBXX:4:1101:4594:1226 2:N:0:TGGATCGA+TATCGCAC
GGAAAACCCAACCNCCTTTATGGGACACTATTTGCATGAAGTTGCCAGAAGACATCCTTATTTCTATGCCCCAGAACTTCTTTACTATGCTGAGCAGTACAATGAGATTCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTATCGC
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJFJJAJJJJFFFJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJFJJJJFJJF
@J00170:103:HMYG2BBXX:4:1101:6055:1226 2:N:0:TGGATCGA+TNTCGCAC
GTCAGACCATCACNTTCAGTAGGGACTTGTCTTGGCTAACAGCAGTGTATCCATCTGGTCAGCTCTACTGAGGGAAGGGGCCAAGTTACTGCTGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTATCGCACGTGTAGATCTCGGT
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJA

Starting FASTQC command


Processing 8_S30_R1_001.fastq

Printing command:
fastqc --outdir 8_S30_R1_001.fastq

Analysis complete for 8_S30_R1_001.fastq

Processing 8_S30_R2_001.fastq

Printing command:
fastqc --outdir 8_S30_R2_001.fastq

Analysis complete for 8_S30_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 11G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:58 .
drwxrwxrwt. 81 root   root      112K Jul 14 19:56 ..
-rwxr-xr-x   1 kkarri waxmanlab 5.4G Jul 14 19:56 8_S30_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 5.4G Jul 14 19:56 8_S30_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:05 G167_M8_FASTQC
==========================================================
Finished on : Sat Jul 14 20:05:24 EDT 2018
0 hours, 9 minutes and 12 seconds elapsed.
==========================================================