-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M13
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 10:43:48 EDT 2018
Running on node : scc-wg2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177141
Current job name : Step_02_LZ_M13
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177141.1.w

Loading required modules...


List files in scratch directory:

total 929M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:43 .
drwxrwxrwt. 32 root   root       80K May 11 10:43 ..
-rw-r--r--   1 kkarri waxmanlab 929M May 11 10:43 LZ_M13.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:43 LZ_M13_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729556.1 SN390:1085:C9V75ACXX:7:1109:1471:1950 length=33
NGTAAATAATGTGGTTAGGGCTCCGAGGCAAAG
+SRR6729556.1 SN390:1085:C9V75ACXX:7:1109:1471:1950 length=33
#1:DDDDEFHDFFGHIJIJEHIJIIBGGIDHAG
@SRR6729556.2 SN390:1085:C9V75ACXX:7:1109:1493:1952 length=33
NTCGTTGTACTGCTTGGAGGGCCTGTAAGTGAG
+SRR6729556.2 SN390:1085:C9V75ACXX:7:1109:1493:1952 length=33
#1=DDDD;DFHHF@GHGGHI@AGHIEGCDHHGG
@SRR6729556.3 SN390:1085:C9V75ACXX:7:1109:1303:1961 length=33
ATCTCCTCCAGCCGCTTTCTTCGCTCTTGTCTC
+SRR6729556.3 SN390:1085:C9V75ACXX:7:1109:1303:1961 length=33
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJ
@SRR6729556.4 SN390:1085:C9V75ACXX:7:1109:1716:1928 length=33
NCGCAGCTCCGGGGTGATATCTGGCCTTTTGGC
+SRR6729556.4 SN390:1085:C9V75ACXX:7:1109:1716:1928 length=33
#4=DDFFFHHHHGI@EGGIIJGIJJJJIIJGII
@SRR6729556.5 SN390:1085:C9V75ACXX:7:1109:1650:1933 length=33
NTGTCTTCTCGGAGATGGTATCAAATTTAAAAA
+SRR6729556.5 SN390:1085:C9V75ACXX:7:1109:1650:1933 length=33
#4=DDFFFHHHHHIGIJJCHHIJJJGJJJJJJJ

Starting FASTQC command


Processing LZ_M13.fastq

Printing command:
fastqc --outdir LZ_M13.fastq

Analysis complete for LZ_M13.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.9G
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:44 .
drwxrwxrwt. 32 root   root       80K May 11 10:43 ..
-rw-r--r--   1 kkarri waxmanlab 4.9G May 11 10:43 LZ_M13.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:45 LZ_M13_FASTQC
==========================================================
Finished on : Fri May 11 10:45:34 EDT 2018
0 hours, 1 minutes and 46 seconds elapsed.
==========================================================