-----------------------
Start of variable list:
-----------------------
Sample_ID:
H6-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 19:46:10 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791249
Current job name : Step_02_H6-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/8791249.1.linga

Loading required modules...


List files in scratch directory:

total 100M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:46 SRR6575919_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:46 SRR6575919_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575919_1.fastq <==
@SRR6575919.1 1/1
CTTCACAGCATTCTCCATATTACAGTCTGAGAAGATGATGAGAGGAGATTTGCCCCCAAGTTCCAAAGTAATGGGCTTGACTCCCTTAGCGGACATCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575919.2 2/1
AATGTGATCCCTTCCGGCGGTCGGTATAAAATCAGGCAGTTTTTGATCACGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575919.3 3/1
GCTGGGAGCTGCTTTCATCTCTGGAGGCTCCAGGAGCTTCAGGTCCATGTTGCATCTGTGGTCCCTACAGCGCGGTCACCTGCAGGCTCTGAGGAGCAGA
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575919.4 4/1
GGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGAT
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575919.5 5/1
GTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFF

==> SRR6575919_2.fastq <==
@SRR6575919.1 1/2
NTCCCTTCCAGATCGCCTGTTGGAAGTCTGCTCCGGCTCTGGCTTGTGGTAATGCCATGATCTTTAAGCCTTCTCCCTTCACGCCTGTGTCTGCTCTGCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575919.2 2/2
ACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCCATAGAAGCCGATACCGTGAAAGAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFFFFFFFFFFFFF-FFF8F
@SRR6575919.3 3/2
NGTCTTCAATAACAAGAACAGTGGCTTCTGGCACAGCAGCCTCATTGACCGGAACCTCATAGATTATTTTGTCCCCTTCCTGCCCCTGGAGTACAAGCAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6575919.4 4/2
NGTTTGCACAACTATGTGAGGAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575919.5 5/2
CTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGAATATTAAAGTTGCTGCAGTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFF-FFFFF-FFF8FFF-F-FF

Starting FASTQC command


Processing SRR6575919_1.fastq

Printing command:
fastqc --outdir SRR6575919_1.fastq

Analysis complete for SRR6575919_1.fastq

Processing SRR6575919_2.fastq

Printing command:
fastqc --outdir SRR6575919_2.fastq

Analysis complete for SRR6575919_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 574M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 287M Oct 12 19:46 SRR6575919_1.fastq
-rw-r--r--   1 kkarri waxmanlab 287M Oct 12 19:46 SRR6575919_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:06 EDT 2018
0 hours, 0 minutes and 56 seconds elapsed.
==========================================================