-----------------------
Start of variable list:
-----------------------
Sample_ID:
E14-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 19:41:27 EDT 2018
Running on node : scc-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790758
Current job name : Step_02_E14-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/8790758.1.linga

Loading required modules...


List files in scratch directory:

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root      132K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6575481_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6575481_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575481_1.fastq <==
@SRR6575481.1 1/1
ATTCTTCAACGAATTAGAAGGAGCAATTTGCAAATTCATCTGGAATAACAAGAAACCTAGGATAGCAAAAAGTCTTCTCAAGGATAAAAGAACTTCTGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFF-FFF-
@SRR6575481.2 2/1
GTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575481.3 3/1
TCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTAAAATATTTTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F----F----FF---F-
@SRR6575481.4 4/1
TGCCAGTAGAAGGTGTGGCCCAGATTAAAGGTAGATCTCACCTCAGAATATCTGGATTAGATGTATATCTTTCTATCTCAAAGATCCAGATTAGAAGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575481.5 5/1
CAACTGACTTCTATTGATGAGTGAGTGGGAGGTCTGCTTGAAAAAAATCACTTTGAAGGACATCCTGTTTACAGAATAGGTGGGACATAGCTGTGAGTGT
+
FFFF-FFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFF8FFFFFFF-FFF-FFFF-F-FFFFFFF--FFFFF-F--FFF-FFFFFFFFFFFFF-FFFFFF

==> SRR6575481_2.fastq <==
@SRR6575481.1 1/2
GGAGATAAGTATGGATCAATTCGCATTCTTCTACACGATAACAACCAGTTGTGCCTGCACCAATTGTTGAAAATGCTGTCTTTCTTCCACTGGATGGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575481.2 2/2
CATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8F-FFFFF-FFF
@SRR6575481.3 3/2
GATGAAACAGAATTTAGAAACTTTATCGTTTGGCTTGAAGACCAGAAAATCAGACACTACAAGATTGAAGACAGAGGTAACTTGAGAAACATCCACAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFF88FFFF8-FF8-8F
@SRR6575481.4 4/2
ACTAAAACCCAAATGGCTGGGAACACCTGTGAGGGATTTTTTTTTCTTAATTAAATCATTTGAGGTGAGAAGACCCACTTCTAATCTGGATCTTTGAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575481.5 5/2
GCATTATGGGTGCTAGGAATTAAATCTGGGTCCTCTAGAAGAGCAGACAGTGTTCTTAACTGCTGAGCTGTCTCCAGCCCTGAGAAGAGATATCCTGTGC
+
8F8-8FFFFFFF8FFFFFFFFFFF8FF8FFFFF8FFF-FFFFF-FFFFFFFFFFFFFFFFF--FF-FFF-FFFFFFFFFF-FFFFFFFFF-F8F8F8F8F

Starting FASTQC command


Processing SRR6575481_1.fastq

Printing command:
fastqc --outdir SRR6575481_1.fastq

Analysis complete for SRR6575481_1.fastq

Processing SRR6575481_2.fastq

Printing command:
fastqc --outdir SRR6575481_2.fastq

Analysis complete for SRR6575481_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 212M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root      132K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 106M Oct 12 19:41 SRR6575481_1.fastq
-rw-r--r--   1 kkarri waxmanlab 106M Oct 12 19:41 SRR6575481_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:44 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================