-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M18
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-wh3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177146
Current job name : Step_02_LZ_M18
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177146.1.w

Loading required modules...


List files in scratch directory:

total 596M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:43 .
drwxrwxrwt. 26 root   root       68K May 11 10:43 ..
-rw-r--r--   1 kkarri waxmanlab 596M May 11 10:43 LZ_M18.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:43 LZ_M18_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729561.1 SN390:1085:C9V75ACXX:8:2209:1221:1923 length=33
NCATATCCTTGACTTTAAACACATGATGCTCAT
+SRR6729561.1 SN390:1085:C9V75ACXX:8:2209:1221:1923 length=33
#1:BDFDDHHHBFIIIGIIFIIIIIGGFFHIII
@SRR6729561.2 SN390:1085:C9V75ACXX:8:2209:1051:1924 length=33
NACATCCCGGGGGCAGTTGATGTCCAGTGACTT
+SRR6729561.2 SN390:1085:C9V75ACXX:8:2209:1051:1924 length=33
#4=DFFFFHGHHHJJJIJJJIJJJJJIIIJJJJ
@SRR6729561.3 SN390:1085:C9V75ACXX:8:2209:1087:1986 length=33
GCCTTCATAATGTGCCTTCACCTTGTCTCCTTT
+SRR6729561.3 SN390:1085:C9V75ACXX:8:2209:1087:1986 length=33
C@@FFFFFHHHHHIJJJJJJJJJJJJJJJJJIJ
@SRR6729561.4 SN390:1085:C9V75ACXX:8:2209:1405:1920 length=33
NCTCCTCTCCGCTGTACCAGGTAAGGCTTCTGA
+SRR6729561.4 SN390:1085:C9V75ACXX:8:2209:1405:1920 length=33
#1=DDFFFHHHHHJJJJJJIIBHIJJJIJJIJJ
@SRR6729561.5 SN390:1085:C9V75ACXX:8:2209:1386:1982 length=33
CTCTGAGCCATCCTCCTCGGTGGCCTTCTTCCC
+SRR6729561.5 SN390:1085:C9V75ACXX:8:2209:1386:1982 length=33
CCCFFFFFHHHHHJJJJJJJHJJJJJJJJIJJJ

Starting FASTQC command


Processing LZ_M18.fastq

Printing command:
fastqc --outdir LZ_M18.fastq

Analysis complete for LZ_M18.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 10:44 .
drwxrwxrwt. 26 root   root       68K May 11 10:43 ..
-rw-r--r--   1 kkarri waxmanlab 3.4G May 11 10:43 LZ_M18.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:45 LZ_M18_FASTQC
==========================================================
Finished on : Fri May 11 10:45:01 EDT 2018
0 hours, 1 minutes and 13 seconds elapsed.
==========================================================