-----------------------
Start of variable list:
-----------------------
Sample_ID:
C2-MAA100039-3_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 19:44:28 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791020
Current job name : Step_02_C2-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791020.1.linga

Loading required modules...


List files in scratch directory:

total 65M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6576841_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:44 SRR6576841_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576841_1.fastq <==
@SRR6576841.1 1/1
ACGTAAATCCATATTAAATCCAAGACAATGTTTTACATCATTCAGGTCAACACCTTTCTCTTTCATGGAAGCTTTTTACAAGACTTAGACAATTTCATAT
+
-8F--8FFF--FFFFFFF8FFFF8FFFFF8F88FFF8F8FFF8FFFF-FF-FF-FF-FFF--F-F-FFFFF-F-F-F-FFFFF--FFF--FFF-FFFF--
@SRR6576841.2 2/1
GACTACACCACAGGCCAGGTGTTTGATTTGTCTGAGAAGTTAGAGCAGTCGGAAGCCCAACTGGGACGTGGCAGTTTCATGGTGGGCTTAGAAACACATG
+
FF--FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-F-FFFFFFFF
@SRR6576841.3 3/1
GCACCTAAAATAGATGACACTCCAGCTAAATGAAGGGAGAAAATTGTTAGGTCTACTGATGCTCCTGCATGGGCTAGATTTCCGGCTAGAGGTGGGTAGA
+
F-FFF-FFF-FFFF8-FFFFFFFFFFF8FFFFFFFFFFF8FFFF-FFFFF-F-FFFFFFF-FFFFFFFF-FFFFF--FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576841.4 4/1
GTGCCTACGGCTACAGTAACCCTAAGATCCTAAAACAGAGCATGACCTTGAACCTGGCCGACCCGGTGGGCAGTCTGAAGCCGCACCTCCGCGCCAAGAA
+
F-FFFFFFFFFFFFFFFFFFFFF88FFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576841.5 5/1
AGCAGGGTGTGTGCTGAGACCTCTGCCTAAAAAGAAGCACCCGGTCTTTTTCCAGGGCCCTGACTGAATGGGCCACATGAAACCAATGTCATTGTAGACA
+
-FF-FFFFFFFFFFFFFFFFFFF8FFFFFFFF8FF-FFFFFF8FFFFF-F-FFFF-FF-FFFFFFFFF-FFFFFFF--FFFFFFFFFF-FF-F--FFFF-

==> SRR6576841_2.fastq <==
@SRR6576841.1 1/2
NCAGTGTAATGGTGACAAATACTGTGGAGATTATTCTGATGAGAATGACTGTGACGTTGACCCACGCACCCCATGCCGTGACCGAGTAGCTGAAGAATCA
+
#--F--FFFF8FF8F-8F-8F8FFFFFF-FFFF--FFFFFFFFFF-FF-F--FF-F-FFF-FFFF-FF-FFF--FFFF--F-F-FFF-FF-FFF-FFFFF
@SRR6576841.2 2/2
CTAATACTCAGGACACCACACAGCACCTTAGTCTTCTAATCTGAGTTTTGGTAAGTGGGTTAAAAGTGTTTCTTGAGCTTCTTTTCCTTCCACACACCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFFF-FFFFFFF-FFF-FFF-FFFFF-FF-FFF-FFFFF-FFFFF-FFFFFFF-FFF8F88-
@SRR6576841.3 3/2
ATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCACTAATAATCTGAGCCCCAGATATAGCATTCCCACGAATAAATA
+
FFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFF-FFFF-FF-FF-FFFFFF-FFFF-FFFFFFFF-FFFFFFF--FFFFFFFFFF--F8-
@SRR6576841.4 4/2
TTGCTGGACTGGATGATCAGGCGCTCCAGCTCCGGCGACGCCAGCTTGAGCAGCCCGACGTCGGGCGACGTGAGAAGGTCCGAGTTCTTGGCGCGGAGGT
+
FF--FFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFFFF
@SRR6576841.5 5/2
GCCCAGGCTGGCCGTGGACTCCCAGCTTCCTAAAGTACTGAGCTTATAGCTGTGAGTTACCAAGCCTGGCTAAAGTTTATGTTTTATTCAGTAAATGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFFF8FFFFFF-F

Starting FASTQC command


Processing SRR6576841_1.fastq

Printing command:
fastqc --outdir SRR6576841_1.fastq

Analysis complete for SRR6576841_1.fastq

Processing SRR6576841_2.fastq

Printing command:
fastqc --outdir SRR6576841_2.fastq

Analysis complete for SRR6576841_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 295M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 148M Oct 12 19:44 SRR6576841_1.fastq
-rw-r--r--   1 kkarri waxmanlab 148M Oct 12 19:44 SRR6576841_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:02 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================