-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M9
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 : 5524735
Current job name : Step_02_G166_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5524735.1.linga

Loading required modules...


List files in scratch directory:

total 1.6G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:40 .
drwxrwxrwt. 47 root   root       84K Apr 22 19:38 ..
-rw-r-----   1 kkarri waxmanlab 765M Apr 22 19:39 G166_M9.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 804M Apr 22 19:40 G166_M9.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:40 G166_M9_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G166_M9.R1.fastq <==
@A00296:19:H75HLDSXX:4:1101:5014:1000 1:N:0:AGTCAA
NCGGAGAAGGCCTGAGACCTCGGGGAGAGGGAGGTAGACATCGACCGGAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:12102:1000 1:N:0:AGTCAA
NGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCGCGGATGCC
+
#FFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,,,F,,F,,F
@A00296:19:H75HLDSXX:4:1101:16206:1000 1:N:0:AGTCAA
NAGACACAAACGGGAAGGCACACAGCCAGACGGAGCACCGGAGGCACACC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:18304:1000 1:N:0:AGTCAA
NGGGCGCCACGGGGGCGCGGTGGGTTCCCACGGGGCACGGGACCGAGAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:28320:1000 1:N:0:AGTCAA
NGGAAGCGGAGGCGGAGGACGAACCCACCGTGAACTCGGGCGGCGCCATT
+
#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF

==> G166_M9.R2.fastq <==
@A00296:19:H75HLDSXX:4:1101:5014:1000 2:N:0:AGTCAA
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:12102:1000 2:N:0:AGTCAA
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:16206:1000 2:N:0:AGTCAA
GCATACCCTTCCCGTCTGGTGTGTGCACGCGCTGTTTCTTGTAAGCCTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:18304:1000 2:N:0:AGTCAA
CGGCCCGGGCGACCCCACACACAACGGAGCATTTACAACAAAAACCGCAA
+
F,,,F,:::,,,::FF:,:,F,,,,,,,,:,,,,,FF::,:FFFF:,,:,
@A00296:19:H75HLDSXX:4:1101:28320:1000 2:N:0:AGTCAA
GGTGTGGCGGTGGGGGCTCCGGTCGATGTCTACCTCCCTCTCCCCGAGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing G166_M9.R1.fastq

Printing command:
fastqc --outdir G166_M9.R1.fastq

Analysis complete for G166_M9.R1.fastq

Processing G166_M9.R2.fastq

Printing command:
fastqc --outdir G166_M9.R2.fastq

Analysis complete for G166_M9.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 7.7G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:41 .
drwxrwxrwt. 41 root   root       84K Apr 22 19:46 ..
-rw-r-----   1 kkarri waxmanlab 3.9G Apr 22 19:39 G166_M9.R1.fastq
-rw-r-----   1 kkarri waxmanlab 3.9G Apr 22 19:40 G166_M9.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:47 G166_M9_FASTQC
==========================================================
Finished on : Mon Apr 22 19:47:17 EDT 2019
0 hours, 9 minutes and 51 seconds elapsed.
==========================================================