-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M4
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/LZ
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 16:46:24 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/02_FASTQC
Current job ID : 6135830
Current job name : Step_02_LZ_M4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6135830.1.linga

Loading required modules...


List files in scratch directory:

total 601M
drwx------   3 kkarri waxmanlab 4.0K May  9 16:46 .
drwxrwxrwt. 16 root   root       36K May  9 16:46 ..
-rw-r--r--   1 kkarri waxmanlab 601M May  9 16:46 LZ_M4.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 16:46 LZ_M4_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729590.1 SN390:985:C970NACXX:3:1102:1340:1881 length=33
NTGGACCTGGTCAGACAGCGTCTGCACCCAGCN
+SRR6729590.1 SN390:985:C970NACXX:3:1102:1340:1881 length=33
#1=DFFFFHHHHHJJJJJJJJJJJJJJJJJJI#
@SRR6729590.2 SN390:985:C970NACXX:3:1102:1267:1892 length=33
NTTGGTGTAAGCAACTAAAAGTGGCAGAGGCGN
+SRR6729590.2 SN390:985:C970NACXX:3:1102:1267:1892 length=33
#1=DDDDDFHFDHHGIGIIEHCHIIICHIICE#
@SRR6729590.3 SN390:985:C970NACXX:3:1102:1446:1967 length=33
CGGGGATGTGGCTCCTACCCGGATAAAAGGAAG
+SRR6729590.3 SN390:985:C970NACXX:3:1102:1446:1967 length=33
CCCFFFFFHHHFHJJEGIJJJJIJJJJJJJJJG
@SRR6729590.4 SN390:985:C970NACXX:3:1102:1747:1993 length=33
CCCGGGGCTCCCGCCGGCTTCTCCGGGATCGGT
+SRR6729590.4 SN390:985:C970NACXX:3:1102:1747:1993 length=33
BCCFFFFFHHHHHJJJJJJJJJJJIJJIJJHHC
@SRR6729590.5 SN390:985:C970NACXX:3:1102:1849:1899 length=33
NTCGGCATGTATTAGCTCTAGAATTACCACAGT
+SRR6729590.5 SN390:985:C970NACXX:3:1102:1849:1899 length=33
#4BDFFFFHHHHHJJJJJJJJJJJJJJJIJJJI

Starting FASTQC command


Processing LZ_M4.fastq

Printing command:
fastqc --outdir LZ_M4.fastq

Analysis complete for LZ_M4.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.3G
drwx------   3 kkarri waxmanlab 4.0K May  9 16:46 .
drwxrwxrwt. 15 root   root       36K May  9 16:47 ..
-rw-r--r--   1 kkarri waxmanlab 3.3G May  9 16:46 LZ_M4.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 16:47 LZ_M4_FASTQC
==========================================================
Finished on : Wed May  9 16:47:41 EDT 2018
0 hours, 1 minutes and 17 seconds elapsed.
==========================================================