-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M22
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-we2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177150
Current job name : Step_02_LZ_M22
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177150.1.w

Loading required modules...


List files in scratch directory:

total 719M
drwx------   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 27 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 719M May 11 10:46 LZ_M22.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:46 LZ_M22_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729565.1 SN390:1085:C9V75ACXX:5:2301:1440:1932 length=33
NTTCCATGGCCACCGTCCTGCTGTCTATATCAA
+SRR6729565.1 SN390:1085:C9V75ACXX:5:2301:1440:1932 length=33
#4BDFFFFHHHHHJJIJJJJJJJJJJJJJJJJJ
@SRR6729565.2 SN390:1085:C9V75ACXX:5:2301:1256:1933 length=33
NATCATTGCAGTCAATTTCCTGCGCTTCTTCTC
+SRR6729565.2 SN390:1085:C9V75ACXX:5:2301:1256:1933 length=33
#1=DBDFFHGFHHIJJJJIGHIIGJJJIJJJJJ
@SRR6729565.3 SN390:1085:C9V75ACXX:5:2301:1408:1956 length=33
CTGAGACAGGGCCACCTGGCTGGATATGGATGT
+SRR6729565.3 SN390:1085:C9V75ACXX:5:2301:1408:1956 length=33
CCCFFFFFHHHGHIJJJJJIIJIFFGHGJGHIH
@SRR6729565.4 SN390:1085:C9V75ACXX:5:2301:1346:1966 length=33
CTCCATTAAGACAATAGTACCACATTAATTAAA
+SRR6729565.4 SN390:1085:C9V75ACXX:5:2301:1346:1966 length=33
CCCFFFFDFHAHHHHGBCFGIGJIGGEEHIIHI
@SRR6729565.5 SN390:1085:C9V75ACXX:5:2301:1614:1912 length=33
NCGAGAAGAAACTGGACACAGCTTTCTCAAGAG
+SRR6729565.5 SN390:1085:C9V75ACXX:5:2301:1614:1912 length=33
#11=?ADDAFFDDFEFFFCGG;BFFHIIFFFFG

Starting FASTQC command


Processing LZ_M22.fastq

Printing command:
fastqc --outdir LZ_M22.fastq

Analysis complete for LZ_M22.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.7G
drwx------   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 27 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 3.7G May 11 10:46 LZ_M22.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:47 LZ_M22_FASTQC
==========================================================
Finished on : Fri May 11 10:47:44 EDT 2018
0 hours, 1 minutes and 22 seconds elapsed.
==========================================================