-----------------------
Start of variable list:
-----------------------
Sample_ID:
H2-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 19:46:12 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791238
Current job name : Step_02_H2-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/8791238.1.linga

Loading required modules...


List files in scratch directory:

total 153M
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 H2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  72M Oct 12 19:46 SRR6575910_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  81M Oct 12 19:46 SRR6575910_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575910_1.fastq <==
@SRR6575910.1 1/1
GCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575910.2 2/1
GTCCACACCACGGACTTTCCCGGTAACTACGCCGGTTATGATGATGCCTGGGACCAGAACCGCTTCGAGAAGAATTTCCGTGTGGACGTGGTGCAAATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6575910.3 3/1
CTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575910.4 4/1
TCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGTGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF
@SRR6575910.5 5/1
GTGTAGTATTTCACATGGATGGCTGAGACCCTGCTTCTTCTGTGAGCAAAAAGGTCCTCCTGTCCTATGTACCTGCATCTGGTAGTCCTTTATGAATGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575910_2.fastq <==
@SRR6575910.1 1/2
TTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTAGGATGTGG
+
8FFFFFFFFFFFFFF-FFFFFFFFFF-FFFFF--FFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFF8FFFFFFFFFFF-FFF-8FFF
@SRR6575910.2 2/2
AGATATAATGGTCCCGAACCCGGGCAAGCCGCACAGCCTTCTTGAGTTTCTCATGCCGGAAGATTTCCCTGCTGAAGGTATCCAGCCGAGCATTGGCCAC
+
F--F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF-F-FF-FFFFFFF-FFFFFFFFFF-F-FFFFFFFFFFFF-FFFF8F
@SRR6575910.3 3/2
GCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575910.4 4/2
GTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGA
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575910.5 5/2
GAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAAACACTGCAAAAAAAATTTATTAGTTGTTAAACATTTAATTTTTTTAAAATTTATAAATT
+
F8FFFFF-FFFFFFFFFFFFFFF8FFFFFFFFFFF-F----FF------FFFFFF--F--FF--------F--F-FFFFFFFFFFFFFFF--F---FF-F

Starting FASTQC command


Processing SRR6575910_1.fastq

Printing command:
fastqc --outdir SRR6575910_1.fastq

Analysis complete for SRR6575910_1.fastq

Processing SRR6575910_2.fastq

Printing command:
fastqc --outdir SRR6575910_2.fastq

Analysis complete for SRR6575910_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 828M
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 19:47 H2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 414M Oct 12 19:46 SRR6575910_1.fastq
-rw-r--r--    1 kkarri waxmanlab 414M Oct 12 19:46 SRR6575910_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:18 EDT 2018
0 hours, 1 minutes and 6 seconds elapsed.
==========================================================