-----------------------
Start of variable list:
-----------------------
Sample_ID:
H4-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 19:46:11 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791244
Current job name : Step_02_H4-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/8791244.1.linga

Loading required modules...


List files in scratch directory:

total 56M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:46 SRR6576972_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576972_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576972_1.fastq <==
@SRR6576972.1 1/1
CTATTAAAAAGAAAAAGGTACCAGGTAATTCTATTTGGGAAACGAATGCACTAACTTTAAAGAAATTGAAAATCCAGGTGGATAGTCTTAACAGAGGCAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFF
@SRR6576972.2 2/1
CATGAGAAGAAGTGGAGAAGCCATGGAGCCTCAGCAGGGCTAAGGTGGGGCTGGGGCTCCAGGCCTGATCCTCCATCCTTTACTGTCCCAGGCAGAGGCC
+
F8FFFFFFF-FFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576972.3 3/1
CTGTATGACTGTCCATCCTCCGTTTTCTGTTTTCATGTCACAGTATACTCTGTACGGCTTGATGGAGGTGTCAGGCTGGATGAGATACATTTCGGATGTC
+
FFFFFFF-FFFFFFFFFFFFFFF8FFF8FFFFFF8FFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFF
@SRR6576972.4 4/1
GAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCACGGACTCGAGAAAGAGCTATCAATCTG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFF
@SRR6576972.5 5/1
GAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTG
+
FFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFFF

==> SRR6576972_2.fastq <==
@SRR6576972.1 1/2
NGTATGTGCTGAACAACAGTGGACAGACCAAGCGCAGGGTGCGAGGACAAGCATAGAAAAGGGGACCAAGATTTTACTCAAATGCTTTTCAGAGCCTTTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576972.2 2/2
CCTTATCACAGAGATGGCGCTGCAGGGCCCAGATGTGTGACTGGGCATGTTTCCAGGAAAGAGGCCATCTCTTGGGGGTTTCAGCCATCTTACCCAGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576972.3 3/2
GATCAGAGATTATATATTGATGAGACTGTGAATGATAATATCCCCCTTAATCTTCGTGTGCTCCGCTCAATCCTGGAGGACCTGAGAAGCAAAATACAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576972.4 4/2
GTCTTTGGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8F8FF
@SRR6576972.5 5/2
GTCTTTGGGTACCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCA
+
FFFFFF-FFF8FFFFFFFFFFFFFFFFFFFF-F-FFF-F-FF-FF-F-FFFF-FFFFF-F-F-FFFFFFFFFFFFFF-F--FFF-FFFFFFFFFFFFF8F

Starting FASTQC command


Processing SRR6576972_1.fastq

Printing command:
fastqc --outdir SRR6576972_1.fastq

Analysis complete for SRR6576972_1.fastq

Processing SRR6576972_2.fastq

Printing command:
fastqc --outdir SRR6576972_2.fastq

Analysis complete for SRR6576972_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 296M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 148M Oct 12 19:46 SRR6576972_1.fastq
-rw-r--r--   1 kkarri waxmanlab 148M Oct 12 19:46 SRR6576972_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:45 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================