-----------------------
Start of variable list:
-----------------------
Sample_ID:
H8-MAA100138-3_56_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 19:46:11 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791255
Current job name : Step_02_H8-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791255.1.linga

Loading required modules...


List files in scratch directory:

total 109M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:46 SRR6575923_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:46 SRR6575923_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575923_1.fastq <==
@SRR6575923.1 1/1
GCTCTGTGCAGAGTCCATCATGTCACTCCAGAACGACCTCACCAGAGTCAGAGGGAAGAGGAGATGCATTCTTGGCATCAGGGACATGAGTTGTTCTTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575923.2 2/1
ACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCAAATACATGCCGACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575923.3 3/1
CACAGAACATCACCCTCTTTGCATTCTGTGATGTCTGGCACTCGACGGTACTGTCGGTGGTAGTAGTAGGTTCGGTTCTTGGCATGCTGTCGTTCAATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575923.4 4/1
ACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCAAATACATGCCGACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575923.5 5/1
TGATTGACCGCACGCAATTGATATTAGATATTTTTGCAAAGCGGGCGAGAACGAGAGAAGGCAAACTTCAAATTGAGCTGGCTCAGCTGCAATATGCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575923_2.fastq <==
@SRR6575923.1 1/2
NTGTTTTCAATTTGCCAGTTTGTGGATGATGGGCTTGATTTAAATCGGACCAAGCTGGAATGTGAATCTGCGTGCACAGAAGCATATTCCCAACCTGATG
+
#FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575923.2 2/2
NCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575923.3 3/2
GACCAGGCTGCCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCTGCTGGGATTAAAGGCGTGCGCTACCACGCCCGGCCAGTTTGGGACTACAGACCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFF
@SRR6575923.4 4/2
CCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFF8FF8
@SRR6575923.5 5/2
CTGTAGCCGCTTGGCAGGACCATTTTTCTGGTCATCGGGTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACTCGTCAGGCGGTTGAACC
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8---

Starting FASTQC command


Processing SRR6575923_1.fastq

Printing command:
fastqc --outdir SRR6575923_1.fastq

Analysis complete for SRR6575923_1.fastq

Processing SRR6575923_2.fastq

Printing command:
fastqc --outdir SRR6575923_2.fastq

Analysis complete for SRR6575923_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 627M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 313M Oct 12 19:46 SRR6575923_1.fastq
-rw-r--r--   1 kkarri waxmanlab 313M Oct 12 19:46 SRR6575923_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:05 EDT 2018
0 hours, 0 minutes and 54 seconds elapsed.
==========================================================