-----------------------
Start of variable list:
-----------------------
Sample_ID:
A8-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 19:42:19 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790946
Current job name : Step_02_A8-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/8790946.1.linga

Loading required modules...


List files in scratch directory:

total 66M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 41 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:42 SRR6575738_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:42 SRR6575738_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575738_1.fastq <==
@SRR6575738.1 1/1
GGAGGGAGCTCAGGATGAGGAACTGTACCTGCTACTCAAATTACTGAGGCCAAACTTCTTAGCAACACTTTGCAACATCCTTACAGGGTCGTCGTCCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF-FFFFF
@SRR6575738.2 2/1
CTGCAGGATGCCTGAGGCAAGTTCACCCAGGCGAACTCCACAGAATGTTCCCTACCAGGACCTGCCTCACCTGGTCAATGCAGACGGACAGTACCTCTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575738.3 3/1
GTTTCATACCCAGCAAAAATAAAGACAATTGACTGGGCTGTGATCTCCATGTCAGAAAGGGCTTTATGAGAGTCTTTGTCTTTGGAATTATTATGAGCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575738.4 4/1
TTCTTGTACTGTGACACTCCGGAAAGGAGAAAAACCTGGAGGCCTTCTTGCCATTTCAGTCATATCTAATGCTTGGCATTTCACAGTCGGGACGACTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575738.5 5/1
GCCCTACCTGGACGAATTCCAGAAGAAATGGAAAGAGGATGTGGAGCTCTACCGCCAGAAGGTGGCGCCTCTGGGCGCCGAGCTGCAGGAGAGCGCGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575738_2.fastq <==
@SRR6575738.1 1/2
NGTACACAGATACCTGTGACTTGTTAACTCATGGCTTCAAACCAAGAATGATCGTGAAGAGAAAGGCAGAAGACTGTGAGGGCTCCCCAGATTCTCATCT
+
#FFFFFFFFFFFFFFFFFFF8FFF-FFFFFFF-FFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF--FFFFFFF
@SRR6575738.2 2/2
NTCTCTGACAAAAACTTGGAAGTCCGACACCACCATCCTCTCTCCCTCACTCTGCCCATGGCCAACATGGTCATGGGCAAATACCAGCATGTCCAGCCCC
+
#-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575738.3 3/2
NTTGCTCTTCTCAGTAGTACTTTTTCCATTCCTGACACCAGTATATGAAATGTTAAATATCTGCATGTTCCCAAAGGATTCAATAGAATTTTTCAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575738.4 4/2
ATGTTATTGAGTTCATAGCCAGAGAAACCAAATGCTCCAAGGAAAGTAACACAGAGCTGGCAGAAGATTGTGAGATCAAGCACCTTGGACAAAGTCTCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575738.5 5/2
CCAGCGCAGGTCTGGCTTTCTCGCCAAGTGTCTTCAGGTGGGTTTTGGCCCTGGTGTGGTACTCGTTCAAGGTAGGGTTGCTCTTGAGCTCAGCCAGGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575738_1.fastq

Printing command:
fastqc --outdir SRR6575738_1.fastq

Analysis complete for SRR6575738_1.fastq

Processing SRR6575738_2.fastq

Printing command:
fastqc --outdir SRR6575738_2.fastq

Analysis complete for SRR6575738_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 358M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 41 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 179M Oct 12 19:42 SRR6575738_1.fastq
-rw-r--r--   1 kkarri waxmanlab 179M Oct 12 19:42 SRR6575738_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:41 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================