-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M24
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/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/infusion/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 10:46:22 EDT 2018
Running on node : scc-wf3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177152
Current job name : Step_02_LZ_M24
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177152.1.w

Loading required modules...


List files in scratch directory:

total 593M
drwx------   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 28 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 593M May 11 10:46 LZ_M24.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:46 LZ_M24_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729567.1 SN390:1085:C9V75ACXX:8:2209:1428:1929 length=33
NGATGCTGTATGGATAGGAAGGGATGATGGTGG
+SRR6729567.1 SN390:1085:C9V75ACXX:8:2209:1428:1929 length=33
#1=DDFFFHHHHHIJJJJJJJJJJJJJJJJIJJ
@SRR6729567.2 SN390:1085:C9V75ACXX:8:2209:1816:1916 length=33
NCCTCCTTGCGCTCAGCCCCACAGTCCTCAGTG
+SRR6729567.2 SN390:1085:C9V75ACXX:8:2209:1816:1916 length=33
#1=DDFFFHHHHHJJJJJJJJJJJHIJJJJJIJ
@SRR6729567.3 SN390:1085:C9V75ACXX:8:2209:2183:1911 length=33
NCCGGGTTCAGGGTCATGGAGACCAGCTGGCTG
+SRR6729567.3 SN390:1085:C9V75ACXX:8:2209:2183:1911 length=33
#1=DDDDDHHHHHFGHIJJJJJJIIJJJGIFGI
@SRR6729567.4 SN390:1085:C9V75ACXX:8:2209:2020:1939 length=33
NGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTG
+SRR6729567.4 SN390:1085:C9V75ACXX:8:2209:2020:1939 length=33
#1:BDFFFHHHHHJJJJJJJJJJJJJHIJJJJJ
@SRR6729567.5 SN390:1085:C9V75ACXX:8:2209:2188:1960 length=33
AGCATTGCCACAGCCTTTGCTATGCTCTCCCTA
+SRR6729567.5 SN390:1085:C9V75ACXX:8:2209:2188:1960 length=33
CCCFFFFFHGHHHJJJJJJJJJJJJJJJJJJJJ

Starting FASTQC command


Processing LZ_M24.fastq

Printing command:
fastqc --outdir LZ_M24.fastq

Analysis complete for LZ_M24.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.3G
drwx------   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 28 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 3.3G May 11 10:46 LZ_M24.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:47 LZ_M24_FASTQC
==========================================================
Finished on : Fri May 11 10:47:34 EDT 2018
0 hours, 1 minutes and 12 seconds elapsed.
==========================================================