-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M33
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-we2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/02_FASTQC
Current job ID : 6177161
Current job name : Step_02_LZ_M33
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177161.1.w

Loading required modules...


List files in scratch directory:

total 733M
drwx------   3 kkarri waxmanlab 4.0K May 11 10:50 .
drwxrwxrwt. 27 root   root       68K May 11 10:50 ..
-rw-r--r--   1 kkarri waxmanlab 733M May 11 10:50 LZ_M33.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:50 LZ_M33_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6729576.1 SN390:1085:C9V75ACXX:7:1109:1209:1949 length=33
NCCATTATCTTCTATCTTTTCTCTCTTGTCAGA
+SRR6729576.1 SN390:1085:C9V75ACXX:7:1109:1209:1949 length=33
#1=DDDFFGBHHHJGGHIIIJJIGIJIJJJJEF
@SRR6729576.2 SN390:1085:C9V75ACXX:7:1109:1503:1976 length=33
GCACCTCGTTGCGGTACTGCCCGAGTCGGTTGC
+SRR6729576.2 SN390:1085:C9V75ACXX:7:1109:1503:1976 length=33
CCCFFFFFHHHHHJHIJJJJJJJIJFHIIHIJJ
@SRR6729576.3 SN390:1085:C9V75ACXX:7:1109:1652:1983 length=33
CTTGCTGACAGTCTCATAATTTGGATCTTTCTG
+SRR6729576.3 SN390:1085:C9V75ACXX:7:1109:1652:1983 length=33
CCCFFFFFHGHHHJJJJJJJJJJJJJJJJJJJI
@SRR6729576.4 SN390:1085:C9V75ACXX:7:1109:1812:1978 length=33
GCACTGAGGAGGTGGTATCCTGCTTCCAGGAAA
+SRR6729576.4 SN390:1085:C9V75ACXX:7:1109:1812:1978 length=33
CCCFFFDEHBFHFHGHIJEFCHIGHIIIIIGII
@SRR6729576.5 SN390:1085:C9V75ACXX:7:1109:2453:1973 length=33
TGCAGAGCCATAATATTGGGTCCAGTGAAACAC
+SRR6729576.5 SN390:1085:C9V75ACXX:7:1109:2453:1973 length=33
;??DD;:++2AADEEA<<CAFDDEACD<@A9CE

Starting FASTQC command


Processing LZ_M33.fastq

Printing command:
fastqc --outdir LZ_M33.fastq

Analysis complete for LZ_M33.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.8G
drwx------   3 kkarri waxmanlab 4.0K May 11 10:51 .
drwxrwxrwt. 27 root   root       68K May 11 10:50 ..
-rw-r--r--   1 kkarri waxmanlab 3.8G May 11 10:50 LZ_M33.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 10:52 LZ_M33_FASTQC
==========================================================
Finished on : Fri May 11 10:52:06 EDT 2018
0 hours, 1 minutes and 25 seconds elapsed.
==========================================================