-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M21
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-wf4
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177149
Current job name : Step_02_LZ_M21
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177149.1.w

Loading required modules...


List files in scratch directory:

total 663M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 24 root   root       24K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 663M May 11 10:46 LZ_M21.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:46 LZ_M21_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729564.1 SN390:1085:C9V75ACXX:5:2301:1224:1913 length=33
NGTGGATAGACTGGAATTGGACTTCTCAGTGAG
+SRR6729564.1 SN390:1085:C9V75ACXX:5:2301:1224:1913 length=33
#1=DDFFFHHHHGIEHGIIJIIJJIJJJJHHII
@SRR6729564.2 SN390:1085:C9V75ACXX:5:2301:1168:1978 length=33
CCCACTTTGCGCCCAGCAGGGGCATCTCTTCGG
+SRR6729564.2 SN390:1085:C9V75ACXX:5:2301:1168:1978 length=33
CCCFFFFFHHHHHJJJJJJJJJHIJJJJJJJJJ
@SRR6729564.3 SN390:1085:C9V75ACXX:5:2301:1690:1926 length=33
NTCATACTTCTGCTCCCCAGGCTGGATGTTCTC
+SRR6729564.3 SN390:1085:C9V75ACXX:5:2301:1690:1926 length=33
#1=DDFFFGHHHHJJJJJJIJJIJIGIIGHIJJ
@SRR6729564.4 SN390:1085:C9V75ACXX:5:2301:1627:1952 length=33
GCACAGGGTAGGCAATAGCTACACAGAGAATCC
+SRR6729564.4 SN390:1085:C9V75ACXX:5:2301:1627:1952 length=33
CCCFFFFFFHHHHJJJJJJJJJJJJJJJJJJJJ
@SRR6729564.5 SN390:1085:C9V75ACXX:5:2301:1764:1958 length=33
GAGGAGACTCCGACCAACTGGGGCAGGCGGCTC
+SRR6729564.5 SN390:1085:C9V75ACXX:5:2301:1764:1958 length=33
CCCFFFFFHHHHGJJJJIJJJJIJJIGIIIIJI

Starting FASTQC command


Processing LZ_M21.fastq

Printing command:
fastqc --outdir LZ_M21.fastq

Analysis complete for LZ_M21.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.4G
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 24 root   root       24K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 3.4G May 11 10:46 LZ_M21.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:47 LZ_M21_FASTQC
==========================================================
Finished on : Fri May 11 10:47:43 EDT 2018
0 hours, 1 minutes and 21 seconds elapsed.
==========================================================