-----------------------
Start of variable list:
-----------------------
Sample_ID:
K17-MAA000377-3_9_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 19:41:26 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790699
Current job name : Step_02_K17-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790699.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576514_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576514_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576514_1.fastq <==
@SRR6576514.1 1/1
GGGGAACCCTTCTCTGGCTTCCTCAGGGGACAGGGGATTGGTTAGATACATGGGAATCATCAGCCTACAGAGGGAAGAGGCTGAGAACACTGAGAGAACA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576514.2 2/1
TGGATATAGTGAGCATAGGTGAGCCATGTAACTGCCTAGAAACAAACACTGTAGTGAATAATGCTTTGAAATCGAACCTTTGTGCCCTATCACCTAATCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576514.3 3/1
TTTCTTACTTTGTGGGACACAAAATATTTCCAAAATGTGAACATCAATGTTGGGTCTTTGTAGGTGGAGGGTAGAAGATTGGACCGTCTTCACAGACCAT
+
FFF-FFFFF8FFFFFFFF8FFFFF8FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576514.4 4/1
GAGCAGAGCTACAGACAGAGACTGGGGGACTCCAGATCACAAGAGCTGAGGTGGTGGATACAATAGTACCATGCTAGACTCTGAGTCGGAGTGGCAGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576514.5 5/1
TTTCTTACTTTGTGGGACACAAAATATTTCCAAAATGTGAACATCAATGTTGGGTCTTTGTAGGTGGAGGGTAGAAGATTGGACCGTCTTCACAGACCAT
+
F-F-F8FFFF8FF8FFFFFF8FFF8F8FFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFF-FFFFFFFFFFF--FFFFFFFFFFFFFF-FF-FFFF-F--

==> SRR6576514_2.fastq <==
@SRR6576514.1 1/2
TTGGAGGCCTGGGCTCTGAGAGCCTTGCCTGAGGCTCATCTCTAGAGTTTGTACGTGCCTGCCCAGACAAACTGTTCCCTCCACATTTTCTGCAGCCAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-F--FF-F-FFFFFFFFFFFF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFF-FFF--8
@SRR6576514.2 2/2
ACATAATTAGAAATGAGTTACAGGGAGGATAAGGACAGGGGCTTCACATTCAATAAATAGAGCTCAAGACGTTACAGATTCATGCTGACAGGGCTGTGGC
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576514.3 3/2
CTCTGGATTACTGGACAATACATGGACTATGGCCCGATAGAGCAGAAGATTGTAACCAGTCCTGGCACTTTAACTTAGATGAGATTAAGGACCTGTTGCG
+
FFFF8F8FFFFFFFFFFFFFFFF8FFFFFFF8F8FFFFF-FFF-FFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFF-F-FF-FFFFFF-8F-FFFFF
@SRR6576514.4 4/2
ACACTCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCAAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGTGGGGGTCTCATCCACACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576514.5 5/2
CTCTGGATTACTGGACAATACATGGACTATGGCCCGATAGAGCAGAAGATTGTAACCAGTCCTGGCACTTTAACTTAGATGAGATTAAGGACCTTTTGCG
+
FFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFF-FFF-FFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6576514_1.fastq

Printing command:
fastqc --outdir SRR6576514_1.fastq

Analysis complete for SRR6576514_1.fastq

Processing SRR6576514_2.fastq

Printing command:
fastqc --outdir SRR6576514_2.fastq

Analysis complete for SRR6576514_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 194M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  97M Oct 12 19:41 SRR6576514_1.fastq
-rw-r--r--   1 kkarri waxmanlab  97M Oct 12 19:41 SRR6576514_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:56 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================