-----------------------
Start of variable list:
-----------------------
Sample_ID:
A2-MAA000907-3_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 19:41:26 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790685
Current job name : Step_02_A2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790685.1.linga

Loading required modules...


List files in scratch directory:

total 19M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 73 root   root      168K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 A2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.2M Oct 12 19:41 SRR6575459_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.6M Oct 12 19:41 SRR6575459_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575459_1.fastq <==
@SRR6575459.1 1/1
GAATTAAATCCGCTTCTTTTACTTCCTCAAGCGTTGAGCGGAATGCAGCAATCAATGTCGTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575459.2 2/1
CCCCAGAACAGCAAGTACTACATAGACCCTGTCTCAAAAATAAAACAAAAATGTGTCCAAGTGAGAAAACCAAAGGCCAGATGCTGTGACGGGGCTGAGC
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575459.3 3/1
CCCCAACACAGCCTTCTGAACTAATAGGAGGACTCTCAGTATTTGGCAGGCAGTCCAGGAGGTCTGTAGTAATTGGGGTCTTTGCCACTGCGGCCATGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575459.4 4/1
CCCTGTCTACTATGCACAGAAGTAATTTTGTTGGTGAATGCAAAGAGACTAAAAAATGGATCAAACTCCGAGGAAGTCGCATCCTGTCTCTTCCACAAAG
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575459.5 5/1
ACTTAATAAGGATCAATGCGCCTACTGCAAAGAAAAGGGACACTGGGCTAAGGACTGCCCAAAGAAGCCACGAGGGCCCCGAGGACCGAGGCCCCAGACC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575459_2.fastq <==
@SRR6575459.1 1/2
NCATATATAGGAAAAGGGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGC
+
#F-F-FFFFFFF8FFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFF8FFFFFFFF-FFFFFFFFFFF
@SRR6575459.2 2/2
GCCGACGCTGGGTGAGGACGGAGCCACCTCCGCCCAAAATAAATTGAGGGTCATGTACCTCCTGGGGGCACCCTGCACCGCCTGATGTCCCAGGGGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575459.3 3/2
GCCATGGAGGGTTTTTTTCATTTATTGGGGAGGCTTTCCAAGGGGCTGGAGACATGTGGCGAGCCTACACTGACATGAAGGAAGCTGGCTGGAAAGATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFF-
@SRR6575459.4 4/2
CAGTTTGTGTCTGGAGCAGACGAGAAAGTTCTTCGTGTTTTTTCTGCTCCTCGGAATTTTGTGGAAAATTTTAGTGTCGTTTCCAGACAGTCACTAAGTC
+
FFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFF-FFFFFFFFFFFFFFF8F
@SRR6575459.5 5/2
ACTTAGGGGTCCAGGATTTTGGGTCAGCACGGAGTGTTGGGCCCCAGTATCTACCAGGAAGGTGACAGGTTGCCCCCCGACTTTGAGGGTTATCCTGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575459_1.fastq

Printing command:
fastqc --outdir SRR6575459_1.fastq

Analysis complete for SRR6575459_1.fastq

Processing SRR6575459_2.fastq

Printing command:
fastqc --outdir SRR6575459_2.fastq

Analysis complete for SRR6575459_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 100M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 73 root   root      168K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 A2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:41 SRR6575459_1.fastq
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:41 SRR6575459_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:45 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================