-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M29
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-wl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177157
Current job name : Step_02_LZ_M29
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177157.1.w

Loading required modules...


List files in scratch directory:

total 765M
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 34 root   root      4.0K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 765M May 11 10:46 LZ_M29.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:46 LZ_M29_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729572.1 SN390:1085:C9V75ACXX:7:1109:1238:1991 length=33
GTCTTAGGTATAGTAAATGTATTGAATCCATCA
+SRR6729572.1 SN390:1085:C9V75ACXX:7:1109:1238:1991 length=33
@BCFFFFFCBFFHGIIIJJJJJJJIJIJGHHHI
@SRR6729572.2 SN390:1085:C9V75ACXX:7:1109:1254:1928 length=33
NTCCAGGGGAGAAGTTGATGGGCAGGTTCCCAG
+SRR6729572.2 SN390:1085:C9V75ACXX:7:1109:1254:1928 length=33
#1=DFFFFHHGHHJIIJGJJJJJJJJDGIJJJJ
@SRR6729572.3 SN390:1085:C9V75ACXX:7:1109:1432:1975 length=33
GTGTCGAGGGCTGACTTTCAATAGATCGCAGCG
+SRR6729572.3 SN390:1085:C9V75ACXX:7:1109:1432:1975 length=33
CCCFFFFFHHHHHJIGIGGIHIJIGIGIJGHIJ
@SRR6729572.4 SN390:1085:C9V75ACXX:7:1109:1708:1956 length=33
GTCATTCAAAAGCAGCATTAGTCCTCTCTGAGG
+SRR6729572.4 SN390:1085:C9V75ACXX:7:1109:1708:1956 length=33
BB@FFFEFGHGHGJJGIIJJJJJJGIIJJIJJI
@SRR6729572.5 SN390:1085:C9V75ACXX:7:1109:2045:1931 length=33
NTCGGATCGTCCTCTGCGTCGTCTACGGAGCTG
+SRR6729572.5 SN390:1085:C9V75ACXX:7:1109:2045:1931 length=33
#1:A1DD@D?ADFFFEE@<)?CCGFF=G7DFF@

Starting FASTQC command


Processing LZ_M29.fastq

Printing command:
fastqc --outdir LZ_M29.fastq

Analysis complete for LZ_M29.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.0G
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 10:46 .
drwxrwxrwt. 34 root   root      4.0K May 11 10:46 ..
-rw-r--r--   1 kkarri waxmanlab 4.0G May 11 10:46 LZ_M29.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:47 LZ_M29_FASTQC
==========================================================
Finished on : Fri May 11 10:48:00 EDT 2018
0 hours, 1 minutes and 38 seconds elapsed.
==========================================================