-----------------------
Start of variable list:
-----------------------
Sample_ID:
B8-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-yf4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790998
Current job name : Step_02_B8-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/8790998.1.y

Loading required modules...


List files in scratch directory:

total 73M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6575764_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:42 SRR6575764_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575764_1.fastq <==
@SRR6575764.1 1/1
GGGAATGGAGCGGACAGGACGCGGAGCCAGTGGGGGACCGCGGGGTTGCCGGAGGAACAGTCCCCCGAGGCGGCGCGTCTGGCGAAAGCCCTGCGCGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575764.2 2/1
CCTAAAATCCAGTGCCTTATGCCAGAACAGGGAGAGAGCGTGCAGACCGTTGGCCAGATAGAGCTGTGCTTCACCAAGGAGGACTTACATTTGCGGAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575764.3 3/1
GCAACAAGCAGCACTTTTCAGGGTCACGTTCGGAGTCAAAGAAGGCTTCGTCTGTTTTGGAGATGTTTACTTGGTTCAAGGTATCAGCAAAAGGTTTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575764.4 4/1
GTACATGGGTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575764.5 5/1
TNTCACCACCATGTCAAACAGAGTCTGCTCACAATATGCTGCATATGGAAAGGAAATATCAAGGCTGAGCCATCTCATAAAACTAGCCCAAAAAGTGCCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-F--FFFFF-FFFFFFFF-FFFF-FF-FF-FFF--FFFFFFFFFFF

==> SRR6575764_2.fastq <==
@SRR6575764.1 1/2
NTCTCTAATCAAGAAAGTTCCTTCTGGAGCCTCTTTTAATTTCTCTTTGGCTTCATTAACAGTCATACTTCCCCAGTACCATCCTGTTTGACTGAGCTCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFF
@SRR6575764.2 2/2
NCGTCTTCACAGACCATCATCCCATGTGTAGAAGCCTCCATGGCCAGCCAGGCTTCCTGCCTGGAGGACAGCTGCTCCCCTGGCTCAGTGCAGTTCCGCA
+
#FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8FFFFF
@SRR6575764.3 3/2
GGGAAAACGGAAGGTTGGATCATTGACTGTCTAGTGGCCATGGTGGTGAAGCTCTCAGAGGTCACATTCAGGCCTCTCTTCTTCAAGCTGTTTGATTGGG
+
FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575764.4 4/2
GTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575764.5 5/2
AAGTAGGTGCACATAAAAATGTTCATGGGTGTGTTTTCTTGACAGCACTCTTCAAACTTAGAATTCTTTTTGGATAAGTTTTGACAGATTTTTATTGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFF-FFFFFFFFFFF-FF-F-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFF

Starting FASTQC command


Processing SRR6575764_1.fastq

Printing command:
fastqc --outdir SRR6575764_1.fastq

Analysis complete for SRR6575764_1.fastq

Processing SRR6575764_2.fastq

Printing command:
fastqc --outdir SRR6575764_2.fastq

Analysis complete for SRR6575764_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 409M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6575764_1.fastq
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6575764_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================