-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M27
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-wh3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177155
Current job name : Step_02_LZ_M27
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177155.1.w

Loading required modules...


List files in scratch directory:

total 827M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 26 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 827M May 11 10:46 LZ_M27.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:46 LZ_M27_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729570.1 SN390:1085:C9V75ACXX:7:1109:1333:1947 length=33
NGCGGCTACTCTTCATGTAGGCAGAGATCTTCT
+SRR6729570.1 SN390:1085:C9V75ACXX:7:1109:1333:1947 length=33
#1=DDFFFDHHHHGGIHFFHIIHDGDFEIGIII
@SRR6729570.2 SN390:1085:C9V75ACXX:7:1109:1456:1982 length=33
CCCTTCTTCAAAAGTGACACTGTCAGGAAGCCT
+SRR6729570.2 SN390:1085:C9V75ACXX:7:1109:1456:1982 length=33
?8?DA?D?BDBCDEI?E<3+3AFFEE@B?@E@D
@SRR6729570.3 SN390:1085:C9V75ACXX:7:1109:1734:1952 length=33
NCTGTGTGGTGAAGGTGTCCGAGACGGAGCCTG
+SRR6729570.3 SN390:1085:C9V75ACXX:7:1109:1734:1952 length=33
#1=DDFDFHHHHHJJHIIJJJJJJJJJJJJJJJ
@SRR6729570.4 SN390:1085:C9V75ACXX:7:1109:1546:1972 length=33
CCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAG
+SRR6729570.4 SN390:1085:C9V75ACXX:7:1109:1546:1972 length=33
CCCFFFDFHHHFHIGHIJIIGIGGIIGGIJCGH
@SRR6729570.5 SN390:1085:C9V75ACXX:7:1109:1593:1978 length=33
GAAGGGATGATGGTGGAGTCCTGGTGAGAAGTC
+SRR6729570.5 SN390:1085:C9V75ACXX:7:1109:1593:1978 length=33
CCCFFFFFHHHHHFHJJJHGIJJJIIJJJIHHJ

Starting FASTQC command


Processing LZ_M27.fastq

Printing command:
fastqc --outdir LZ_M27.fastq

Analysis complete for LZ_M27.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 10:46 .
drwxrwxrwt. 26 root   root       68K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 4.3G May 11 10:46 LZ_M27.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:47 LZ_M27_FASTQC
==========================================================
Finished on : Fri May 11 10:47:57 EDT 2018
0 hours, 1 minutes and 35 seconds elapsed.
==========================================================