-----------------------
Start of variable list:
-----------------------
Sample_ID:
B7-MAA000907-3_11_M-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 19:42:19 EDT 2018
Running on node : scc-wh2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790991
Current job name : Step_02_B7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790991.1.w

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 32 root   root       72K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576059_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:42 SRR6576059_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576059_1.fastq <==
@SRR6576059.1 1/1
CTACAGCTGTTATGCCAGATGGACAATTCAAAGATATCAGCCTAAGTGAATACAAAGGAAAATATGTTGTGTTCTTCTTTTACCCTCTTGACTTTACTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576059.2 2/1
TATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGAGGTATCAACTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-------F-FFF--F-
@SRR6576059.3 3/1
GGGCACGGCACCTGGGCGGCGGCCGCGACCCGGCCGTCCTCGACCAGGGCGACCTTGACGTGGACCCCGCCGAGGTCCCACCCGATCGTCGGTGGGTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFF-FF-FFFFFFFFFFFF-F-F--F---FFFFFF
@SRR6576059.4 4/1
CACTCACACCGCGCTCGGCGCCCTCGCGTGCCCCTGCCTTGTACACAGCTAGGCGCTTCTGCAGATCCTCGGCATCCCGCATCAAGCGCTTGCGCATCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576059.5 5/1
GCTCTCGGGGGCTCTCACCGGGCTCACACGGGTCCGAAGATTCCAGCAGGATGACGCACACATCTTCTGTGCCATGGAGCAGATTGAAGATGAAATCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576059_2.fastq <==
@SRR6576059.1 1/2
NACTTCACCATGTTTGTCAGTGAACTGGAAGGCCTGGACTAGTCGTATAATCTCATCCACAGAGCGGCCAACGGGAAGATCGTTTATTGTTATCTGTCGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFF
@SRR6576059.2 2/2
CCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCAATGCTTACCATGTACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-----FFF--------FF
@SRR6576059.3 3/2
ATCATCGATCGCGCCGAGATCGGCGACGTAGAGGATGGCGGCGGGCCACGCGTCGCGCAGCCCCCGGGCCACCGCGTCGGGCGCCGAGCCCTTTGCCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576059.4 4/2
GCCAGGCTGGGCAAAGAGGTGCAGGCGGCACAGGCCCGACTCGGAGCCGACATGGAGGATCTACGCAACCGACTCGGGCAGTACCGCAACGAGGTGCACA
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576059.5 5/2
CACTATATACTGTGCGAAGAAAATCCAAACAACCTTTGATTTCATCTTCAATCTGCTCCATGGCACAGAAGATGTGTGCGTCATCCTGCTGGAATCTTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576059_1.fastq

Printing command:
fastqc --outdir SRR6576059_1.fastq

Analysis complete for SRR6576059_1.fastq

Processing SRR6576059_2.fastq

Printing command:
fastqc --outdir SRR6576059_2.fastq

Analysis complete for SRR6576059_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 136M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 32 root   root       72K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  68M Oct 12 19:42 SRR6576059_1.fastq
-rw-r--r--   1 kkarri waxmanlab  68M Oct 12 19:42 SRR6576059_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:30 EDT 2018
0 hours, 0 minutes and 11 seconds elapsed.
==========================================================