-----------------------
Start of variable list:
-----------------------
Sample_ID:
G6-MAA100140-3_57_F-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:46:08 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791207
Current job name : Step_02_G6-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791207.1.linga

Loading required modules...


List files in scratch directory:

total 95M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 125 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  49M Oct 12 19:46 SRR6576106_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  46M Oct 12 19:46 SRR6576106_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576106_1.fastq <==
@SRR6576106.1 1/1
ACTACAGATTGCTATAGATAAAACCATCATTCAAAATTATTAAATTAGTTGCATATTTTGAACTACTCTTGATGAAGACAAATAAGGTTTAGCATTGATA
+
FFFFFFF-FFFF-FFFFFFFFFFFFF8FFF8FFFF-F8FFFFF-FFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576106.2 2/1
TNCAAGAGCAGTACTGCTTGCTGAAAAGCTCCTGGATAGGCAACGTCCCAGAGACACATTAGAAGGTAGCTATAACTCACCACACCACTAACTATCCTGC
+
F#F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF-FFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFF-FFFF
@SRR6576106.3 3/1
TGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCCGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAG
+
-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFF
@SRR6576106.4 4/1
TCCATCAGCAGCACCCAGCTGGACAGCATGCTGCAATGATGCACATCAAGCATGCCCGAGAGGGTCATCATGGGCACCTTCACTGTGGTGGACTCGTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576106.5 5/1
CCCCACTTACAGTCACACCAGCATACACAACACCAGCTCCCTGGGATGAAGAGGAGACTGAAGGATCTGCTCACATAGTCACTATGCTCTGGTCTCTGTC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88--FFF-FF-FF-FFF-FFFFF-F-FFFFF-FF-FFF-FFF-FFFFFFFFFFF-FFFFFFF

==> SRR6576106_2.fastq <==
@SRR6576106.1 1/2
NTAACAAACGAAGTAGCTCAGCTCATTCAGGGAGGACGACTTATCAACTACGAGATGAGTAAGCGGCCATCTGCATAGCGGTACAAGGACCAGCTCTTGA
+
#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576106.2 2/2
NTTAANAACTGAAACTTGTGTCCTCCAGCCCCACCCCATCCTGTCATCCCCGTTTCCCAGAATACTACAGCTCTTGCATGACAACCTGAAGTCTCTCCTG
+
#-FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-F--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F-F8
@SRR6576106.3 3/2
NAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGG
+
#FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576106.4 4/2
NTTTTGTGGAGAAGGGAACCCAAGGAAAGATAGTTGAGGCGGTGAAAAAACTGGACCAAGACACAGTTTTCGCCCTGGCGAATTACATTCTCTTTAAAGG
+
#8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576106.5 5/2
NTCCTGATACACTTCGTCCAGCAATGATGAGGGCGTGTGCCGGTCCAAATTTGGAACATCCCATCAAGAGGGCTCCAGTCAATGAGAGGCTGTTTGCAGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576106_1.fastq

Printing command:
fastqc --outdir SRR6576106_1.fastq

Analysis complete for SRR6576106_1.fastq

Processing SRR6576106_2.fastq

Printing command:
fastqc --outdir SRR6576106_2.fastq

Analysis complete for SRR6576106_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 501M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:46 SRR6576106_1.fastq
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:46 SRR6576106_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:56 EDT 2018
0 hours, 0 minutes and 48 seconds elapsed.
==========================================================