-----------------------
Start of variable list:
-----------------------
Sample_ID:
A5-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 19:42:18 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790935
Current job name : Step_02_A5-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/8790935.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:42 SRR6575731_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:42 SRR6575731_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575731_1.fastq <==
@SRR6575731.1 1/1
CNATATATAGTCCGCTGAGATAACCACCATCTCATCAAGTACTTCCAAAATGTTAACATTTCCTCTTAACCAAAAGTCNTGNCCCCAGCCATTTTCTTGA
+
F#FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFF-FF
@SRR6575731.2 2/1
CNTGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCNCTGCTTCCCATGTACTCT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFF--F-FFF#-FFF--FFF-FF-FF-FF
@SRR6575731.3 3/1
CTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575731.4 4/1
GTACATGGGCAACAACGATTCTTTCAATGCGAATCTCTCTACTCGCCGATCCTGGTCTCTCTCTTCTTCTTCTTCGTCTTCGTCGCCGATCAAACTCAGG
+
8FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FF-FFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FF
@SRR6575731.5 5/1
CTGGAAGGGGGCGCCGGAGAGGGTGAGAGCCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCGGCGAGTCGGGTTGTTTGGGAATGCAGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF

==> SRR6575731_2.fastq <==
@SRR6575731.1 1/2
NGTCTNGGCTGAGNACGTGCAAGTACTTGGCTGGTGATTTCTATAGCATGGCTGACCTGCATCACCTTCCTTACATGCACTATTTCATGACCACACCATG
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575731.2 2/2
NGTATNAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACG
+
#F-FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F---FF-F---FF-FFFF-FFF-FF-F-FFFF---FF-FFFFF-FF
@SRR6575731.3 3/2
NGCTCGCGCCCCAGGTTTTGCAGCGACCGCCGCGCCCTCCTACTCATCGGGGCCTGACAATTGCCCCGACGGCCGGGTATAGGTCGCGCGCTTCAGCGCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFF
@SRR6575731.4 4/2
GTATGCACCACTGCCAGTGGCAATATCACTGCAAGCTGTGAACCGCTAACTCTTGGCTTTTTGTAGAGATTAATACCCCACATAAAAAAAACAATTACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-F-FFFFF-FFFFFFF-FF-FFFFFFF-F-FFFFFFF-FFFFFFFFF-FFFFF-F8FF--FF--
@SRR6575731.5 5/2
CCTTACGGGTTTACTGGCCCGTTGACTCGCACACATGTCAGACTCCTTGGTCCGTGTTACAAGACGGGCCGAATGGGGAGCCCGCAGGCCGATGCCAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6575731_1.fastq

Printing command:
fastqc --outdir SRR6575731_1.fastq

Analysis complete for SRR6575731_1.fastq

Processing SRR6575731_2.fastq

Printing command:
fastqc --outdir SRR6575731_2.fastq

Analysis complete for SRR6575731_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 312M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 156M Oct 12 19:42 SRR6575731_1.fastq
-rw-r--r--   1 kkarri waxmanlab 156M Oct 12 19:42 SRR6575731_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:41 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================