-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M4
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-tm2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/02_FASTQC
Current job ID : 5524730
Current job name : Step_02_G166_M4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5524730.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:38 .
drwxrwxrwt. 20 root   root      116K Apr 22 19:37 ..
-rw-r-----   1 kkarri waxmanlab 622M Apr 22 19:38 G166_M4.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 623M Apr 22 19:38 G166_M4.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:38 G166_M4_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G166_M4.R1.fastq <==
@A00296:19:H75HLDSXX:4:1101:6587:1000 1:N:0:ACAGTG
NATCGGAAGAGCACACGTCTGAACTCCAGACAACAAACAAACACAAAACC
+
#FFFFFFFFF::FFFF:FFF,F::::,F,,,,F,F,,,F,,:,:,F,F,,
@A00296:19:H75HLDSXX:4:1101:7871:1000 1:N:0:ACAGTG
NAACATCTTTGGGCGAGGTGATTTTCTGGATCATGGTCCATTTATCAGGG
+
#,FF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,F,F,FFFF
@A00296:19:H75HLDSXX:4:1101:13349:1000 1:N:0:ACAGTG
NCAGGGTTTAGAGTCTGGCTAGCGGTCTTGCTTTGATCCAGTATTTCCTT
+
#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FF
@A00296:19:H75HLDSXX:4:1101:15501:1000 1:N:0:ACAGTG
NTTGATAATGTAGGGAATATTTTTTTCTGAACATGTAATTCTTTTGTAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:17562:1000 1:N:0:ACAGTG
NCTTGTCTGGCATGCTCAAAGTGGAGTTCAAGCACACCACTACACAAGTG
+
#FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> G166_M4.R2.fastq <==
@A00296:19:H75HLDSXX:4:1101:6587:1000 2:N:0:ACAGTG
GATCGGAAGAGCGACGAGTAGGGAAAGATTGTAGAAAAGAGTTAAAAACG
+
FFFFFFFF:FFFF,:,,FFF,,FFFF:F,:,FF,:F,,,F,,F,F,:,,,
@A00296:19:H75HLDSXX:4:1101:7871:1000 2:N:0:ACAGTG
GAACATCTATTGGTCAGTCTGGTCTGATAATCCCAAACTGAGACTCTCAG
+
FFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:13349:1000 2:N:0:ACAGTG
GCAGGGTTCAAAGTCTCTTCTGAGATCCATGCAGTCTCTAAGCTGTAATT
+
FFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:15501:1000 2:N:0:ACAGTG
CTTGATACTGTAGTCAACTATGAAACCTGCATCACCTCTTATGTTCCTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00296:19:H75HLDSXX:4:1101:17562:1000 2:N:0:ACAGTG
CTTGCCTGCCTTAATCTCCCCAGACCTGGTTACAAATGCAAGTAAGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing G166_M4.R1.fastq

Printing command:
fastqc --outdir G166_M4.R1.fastq

Analysis complete for G166_M4.R1.fastq

Processing G166_M4.R2.fastq

Printing command:
fastqc --outdir G166_M4.R2.fastq

Analysis complete for G166_M4.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 6.0G
drwx------   3 kkarri waxmanlab 4.0K Apr 22 19:39 .
drwxrwxrwt. 19 root   root      116K Apr 22 19:40 ..
-rw-r-----   1 kkarri waxmanlab 3.0G Apr 22 19:38 G166_M4.R1.fastq
-rw-r-----   1 kkarri waxmanlab 3.0G Apr 22 19:38 G166_M4.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 19:42 G166_M4_FASTQC
==========================================================
Finished on : Mon Apr 22 19:42:42 EDT 2019
0 hours, 5 minutes and 16 seconds elapsed.
==========================================================