-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M5
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G166_Env
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 22 19:37:26 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/02_FASTQC
Current job ID : 5524731
Current job name : Step_02_G166_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5524731.1.linga

Loading required modules...


List files in scratch directory:

total 1.8G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:40 .
drwxrwxrwt. 47 root   root       84K Apr 22 19:38 ..
-rw-r-----   1 kkarri waxmanlab 903M Apr 22 19:39 G166_M5.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 936M Apr 22 19:40 G166_M5.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:40 G166_M5_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G166_M5.R1.fastq <==
@A00296:19:H75HLDSXX:4:1101:1940:1000 1:N:0:GCCAAT
NCAGGATCAAATGTCACATCCCTGGGATGTTCTTGGAGTAAAGCGCGTGT
+
#FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:5267:1000 1:N:0:GCCAAT
NTGGCATTTACTTGGACACAGGCTTGGCATGATTCCGCCACCTCGTGGAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:11831:1000 1:N:0:GCCAAT
NCCGGACGCGGGGAGGAAGAGGGGAACGACGCGCGGGTGGAGGGGTCGGG
+
#FF,FF,FFFFFF::FF::F,FFFF::,F,:F,F,FFF:F::FFFFF:FF
@A00296:19:H75HLDSXX:4:1101:13295:1000 1:N:0:GCCAAT
NGGCCACCGAGAGAGGATGCATGCGACGAGCACACAGGGAAACCAGAAGA
+
#,,F,F:FFFFFFFFFFF:,F:FFFFFF:FFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:13765:1000 1:N:0:GCCAAT
NGGCCTGGGAGAGGGCAGGGGGTTAGACAGACTTCCCTACGGCTTGAGAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF

==> G166_M5.R2.fastq <==
@A00296:19:H75HLDSXX:4:1101:1940:1000 2:N:0:GCCAAT
CTTCCTCTCAGATGAAAATCCATGCAGCCAGGCATCCGAAGGCTCTGTTG
+
FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:5267:1000 2:N:0:GCCAAT
GATGCCTGACCAGTTCACCTTTGAATTATTAGACTTCCTTCACCAGCTCA
+
:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:11831:1000 2:N:0:GCCAAT
GGGGGGGGCGGGAACACCGCCCCCCCCCGCCCGCCCGGCCCGGGGGGCCC
+
,,,,,,:,,,,,,,,,F,,,,,F,F:F,,,,:,F:F,,,F:,,,,,,,,,
@A00296:19:H75HLDSXX:4:1101:13295:1000 2:N:0:GCCAAT
GCGGATGCTCAGAATGCCCTTGGAAGAGAACCTTCCTGTTGCCGCAGACC
+
FFF:F:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF::FFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:13765:1000 2:N:0:GCCAAT
AGAGAGGGTGCTGGCCTCCCTTAGCTGTGTCCTCTGGCACGACGGGATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF

Starting FASTQC command


Processing G166_M5.R1.fastq

Printing command:
fastqc --outdir G166_M5.R1.fastq

Analysis complete for G166_M5.R1.fastq

Processing G166_M5.R2.fastq

Printing command:
fastqc --outdir G166_M5.R2.fastq

Analysis complete for G166_M5.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.0G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:42 .
drwxrwxrwt. 45 root   root       84K Apr 22 19:47 ..
-rw-r-----   1 kkarri waxmanlab 4.5G Apr 22 19:39 G166_M5.R1.fastq
-rw-r-----   1 kkarri waxmanlab 4.5G Apr 22 19:40 G166_M5.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:48 G166_M5_FASTQC
==========================================================
Finished on : Mon Apr 22 19:48:49 EDT 2019
0 hours, 11 minutes and 23 seconds elapsed.
==========================================================