-----------------------
Start of variable list:
-----------------------
Sample_ID:
E2-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 19:44:30 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791112
Current job name : Step_02_E2-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/8791112.1.linga

Loading required modules...


List files in scratch directory:

total 78M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:44 SRR6576044_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:44 SRR6576044_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576044_1.fastq <==
@SRR6576044.1 1/1
CNAGTGATCCTGTACAACGTCAGGCTCTGCTGTGCATGGATGAAGCAGAAAGATGCGAAGGACCACAGGGACCAAGTCNAGNCATGTCCATCCAGGACAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6576044.2 2/1
GTATCAACGCAGAGTACATGGGAGAGCGCCCGAGAGTTGGCGACAATAGTGGCCATGGCGCGCGCGCTGGCGGATCTATCCGTGAACTTGCAGGTCCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576044.3 3/1
TCCGATTACTCCTCAGATGTTTGGGTATGCTGGGAAAGAACATATGGAAAAATATGGAACAAAAGTTGAACACTTTGCAAAAATTGGATGGAAAAATCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576044.4 4/1
GGAATTGAACTTACTCCTTAGCTCAGGCTTGCCCTCAACCTGCATTCTTTTTGTCTCAAACTCCTAAGTAACTTAGATGACAGGCTCGTGCCGCCAACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576044.5 5/1
AGCCAATGGTGCTTGGGCATGAGGCTGCTGGAACAGTCACAAAAGTAGGAGAGTTGGTGAAACATCTGAAACCAGGAGATCGGGTTGCCATCGAGCCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576044_2.fastq <==
@SRR6576044.1 1/2
NGTCTNTAATNTTNAGAGGCCGCCTGTCCTGGATGGACATGCCTGGACTTGGTCCCTGTGGTCCTTCGCATCTTTCTGCTTCATCCATGCACAGCAGAGC
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576044.2 2/2
NTTCAGCCGGATCTTGTCCCGGCATAGCAACTTGAGGCCTTTGAAGTTCTTCCACTTGGGAGAGACCAGCTTGCCACTGTAAGCCAGGCTCAAGCACTCG
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576044.3 3/2
NTTCTCTTCAAACGTACTGGGTAAGTCAGTCATCATCTCCTGGGCCACAATCTCCACCGCTTTGGACTGCAGGCCGTACTGCTGCACAAACTCCTCGCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576044.4 4/2
AGGTACACCAGTGTCTCCAAATGAGCAGGTATTTTGACTCCAAAAGTGTTGCATTTTTAACCCTTTCAAAGTAAGTCCAAAAGTATTATAAAACCAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576044.5 5/2
GCATAGATCCCCACAGAGAGAGGTTCAATCAGGGCCCCTTCTTCAAAAGTGACACTGTCAGGAAGCTTGTAGCAGAAGTCAGCATTGTGCTTGTAGAATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576044_1.fastq

Printing command:
fastqc --outdir SRR6576044_1.fastq

Analysis complete for SRR6576044_1.fastq

Processing SRR6576044_2.fastq

Printing command:
fastqc --outdir SRR6576044_2.fastq

Analysis complete for SRR6576044_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 440M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 220M Oct 12 19:44 SRR6576044_1.fastq
-rw-r--r--   1 kkarri waxmanlab 220M Oct 12 19:44 SRR6576044_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:55 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================