-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M32
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 10:50:41 EDT 2018
Running on node : scc-wf4
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177160
Current job name : Step_02_LZ_M32
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177160.1.w

Loading required modules...


List files in scratch directory:

total 821M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:50 .
drwxrwxrwt. 24 root   root       24K May 11 10:50 ..
-rw-r--r--   1 kkarri waxmanlab 821M May 11 10:50 LZ_M32.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:50 LZ_M32_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729575.1 SN390:1085:C9V75ACXX:7:1109:1340:1972 length=33
GCTTGCTTAGTGTTCTCAGGATCGAATGGCTTC
+SRR6729575.1 SN390:1085:C9V75ACXX:7:1109:1340:1972 length=33
CCCFFFFFHGHHHJJJIJJJIIJIAGIJ?G)CB
@SRR6729575.2 SN390:1085:C9V75ACXX:7:1109:1513:1938 length=33
NGTTTCGGCAAATGCGCATGCTCAGAACTACTT
+SRR6729575.2 SN390:1085:C9V75ACXX:7:1109:1513:1938 length=33
#1:DDFFFHHHHHJJJJJJJJJJIJJJJJJJJJ
@SRR6729575.3 SN390:1085:C9V75ACXX:7:1109:1803:1932 length=33
NTACTCAAAGGGAAGTGGGTCAGTGCCTTTCCA
+SRR6729575.3 SN390:1085:C9V75ACXX:7:1109:1803:1932 length=33
#1:DDFFFHHHHHJJIJJJHIGIIIJJJJJJJJ
@SRR6729575.4 SN390:1085:C9V75ACXX:7:1109:1861:1943 length=33
NCCTCCAGACGTACTCCAGCTTGGGCGGGGGTC
+SRR6729575.4 SN390:1085:C9V75ACXX:7:1109:1861:1943 length=33
#1=DDFFFHHHFHJJJJJJJJJJJJJJJJFD?B
@SRR6729575.5 SN390:1085:C9V75ACXX:7:1109:1879:1978 length=33
GCTGGTCTGACCAAGCTATCAGGTTTGGGGGGC
+SRR6729575.5 SN390:1085:C9V75ACXX:7:1109:1879:1978 length=33
CCCFFDFFHHHHHJJJJJJJJJJHHIJJJJJDD

Starting FASTQC command


Processing LZ_M32.fastq

Printing command:
fastqc --outdir LZ_M32.fastq

Analysis complete for LZ_M32.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.3G
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:51 .
drwxrwxrwt. 23 root   root       24K May 11 10:52 ..
-rw-r--r--   1 kkarri waxmanlab 4.3G May 11 10:50 LZ_M32.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:52 LZ_M32_FASTQC
==========================================================
Finished on : Fri May 11 10:52:12 EDT 2018
0 hours, 1 minutes and 31 seconds elapsed.
==========================================================