-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M6
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 : 6936716
Current job name : Step_02_G167_M6
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936716.1.linga

Loading required modules...


List files in scratch directory:

total 2.2G
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 1.1G Jul 14 19:56 6_S28_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.2G Jul 14 19:57 6_S28_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:57 G167_M6_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 6_S28_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:2158:1226 1:N:0:GCTTGTCA+GTATGTTC
AGAGGCCAGGATAATAGTATGCCATTCCCCATTAATCTTTTCTACATTAAAGTTCCTTCCCGTAGAACTAGCTTCTTCTGCATGGACACAGACTAGGGTCAGTCCCAAACACAGCAGCAGCAGCATCTTCATTTTGGTAGGGAATAGGATT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJFJFFJJJJJFJJJA<AFF<JJJJ
@J00170:103:HMYG2BBXX:4:1101:3153:1226 1:N:0:GCTTGTCA+GTATGTTC
ATGTCTTCTGGCAACTTCATGCAAATAGTGTCCCATAAAGGGGGTTGGGTTTTCCTTAAAGGAGGTGCACATGGCCTCAGCCTCTGGCCTTTCAAATGGTGGCAGGCTGGGGTTGTCATCTTTGTGTTGCAGGAAACATTCGTTTATTTCG
+
AA<FFJFJJJJFJJFJJJJJJJJJFFFJJJAFJJJJJJJJJ-AF<FAJJJFJJFJFJJJJJFJJJJFJJFAJ777AAAJJ7JJAAFJAF7J<FJA--A7FA-7-FJ<-FAF--7A-AA-F--AF-AFFFA7FJJ77FF<A-<7-A-77<-F
@J00170:103:HMYG2BBXX:4:1101:3376:1226 1:N:0:GCTTGTCA+GTATGTTC
CAGTACTTTAAGGTCTTCACAGAAATGTACTTAAAATCTTCACAGCCAGCTTAGTGAGGATGTTGCCCACTGCCTAACATCTGTAGGGCAGTTGGAGTATTTCTGTAGAGCATTCATAATTTGAGTATTATCCAAAAGTAGTTTCACTAGA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJFJJJJJJJJ
@J00170:103:HMYG2BBXX:4:1101:3579:1226 1:N:0:GCTTGTCA+GTATGTTC
GACAGTTTGCTGTCCATGCTCTGCTGGTACTGAGACTCCAGCTCTTCATTAATTTTCTTGTCTTCTTCCCCTGTTCGGAAGTGAGATGTTGATTTGTGATCTCCTATAACAAGACGACCAGTGTGTTCTTTCTTTCCTGCACCCATGAGAG
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFF<FJJJ
@J00170:103:HMYG2BBXX:4:1101:4655:1226 1:N:0:GCTTGTCA+GTATGTTC
CTCTTCTGCCAGGGTGGATGGCACCGTGGGCTCCCCGATGGCATACTTCTCCTTGGCCCAGGCTAGTTTCTCTTGAATGGCAGCATTGCCGGGCTCCACATGGCGTGCAAACTTAAGGTTGTTTACGGTGTATTCATGACCACAGTAGACT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJFAJFJJJFJJFJFFJJJJJJ7FJF

==> 6_S28_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:2158:1226 2:N:0:GCTTGTCA+GTATGTTC
GTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCA
+
AAAFFJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJFJJ<JJJJJJJJJJFJFJJJJJJFJFJJJFJJJJJFJFJJJJJJJFJFJJJ-AAFFAJJJJJJFJFJJJJJ-FFFF<F<-FJ7AAJFF<AJFFJAFFJJFAF<AJJJ<FJ
@J00170:103:HMYG2BBXX:4:1101:3153:1226 2:N:0:GCTTGTCA+GTATGTTC
TGCCATTCCAAACNTCCGTGAAAACTATGGTGAACTGGCTGACTGCTGTACAAAACAAGAGCCCGAAAGAAACGAATGTTTCCTGCAACACAAAGATGACAACCCCAGCCTGCCACCATTTGAAAGGCCAGAGGCTGAGGCCATGTGCACC
+
AAAFFFFFJJAJJ#FJFA<JFJJJJJJJJ7F<FJJJJFJJJJFAA<FA-AFJJJJJJJAJ<JJAJJJJFJJJJJJJJFJJJJJFFJFJJJFFJJFAF--AFFJJJJF<JJJAJJJJJJFFJ7<FF--AA-77AJFJAFFAA<))77<7<AF
@J00170:103:HMYG2BBXX:4:1101:3376:1226 2:N:0:GCTTGTCA+GTATGTTC
AGTGAAACTACTTNTGGATAATACTCAAATTATGAATGCTCTACAGAAATACTCCAACTGCCCTACAGATGTTAGGCAGTGGGCAACATCCTCACTAAGCTGGCTGTGAAGATTTTAAGTACATTTCTGTGAAGACCTTAAAGTACTGAGA
+
AAAFFJJJJJJJF#JJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJFJJFJFJ
@J00170:103:HMYG2BBXX:4:1101:3579:1226 2:N:0:GCTTGTCA+GTATGTTC
CTCATGGGTGCAGNAAAGAAAGAACACACTGGTCGTCTTGTTATAGGAGATCACAAATCAACATCTCACTTCCGAACAGGGGAAGAAGACAAGAAAATTAATGAAGAGCTGGAGTCTCAGTACCAGCAGAGCATGGACAGCAAACTGTCAG
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJFJJJJJJJJJJAAAJJF
@J00170:103:HMYG2BBXX:4:1101:4655:1226 2:N:0:GCTTGTCA+GTATGTTC
CGCTGCTTGAAGTNTTGGGCCGGCTTCCTCCAGACACAAAAGTCTACTGTGGTCATGAATACACCGTAAACAACCTTAAGTTTGCACGCCATGTGGAGCCCGGCAATGCTGCCATTCAAGAGAAACTAGCCTGGGCCAAGGAGAAGTATGC
+
AAFAFJJJJJJJF#JJJJFJJJFJFJJFJJJJJJJJJJJJJJJJ<AJJJFJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJFJJJJJJJ<JJJFJJJJJJJJJJJJJJFFFFFFFJFJJJFFFJJJFFAJJJ<A<<JJJJJJJJA

Starting FASTQC command


Processing 6_S28_R1_001.fastq

Printing command:
fastqc --outdir 6_S28_R1_001.fastq

Analysis complete for 6_S28_R1_001.fastq

Processing 6_S28_R2_001.fastq

Printing command:
fastqc --outdir 6_S28_R2_001.fastq

Analysis complete for 6_S28_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.9G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:59 .
drwxrwxrwt. 70 root   root      268K Jul 14 20:05 ..
-rwxr-xr-x   1 kkarri waxmanlab 5.0G Jul 14 19:56 6_S28_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 5.0G Jul 14 19:57 6_S28_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:06 G167_M6_FASTQC
==========================================================
Finished on : Sat Jul 14 20:06:01 EDT 2018
0 hours, 9 minutes and 49 seconds elapsed.
==========================================================