-----------------------
Start of variable list:
-----------------------
Sample_ID:
G2-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-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791196
Current job name : Step_02_G2-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/8791196.1.linga

Loading required modules...


List files in scratch directory:

total 61M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:46 SRR6575884_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6575884_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575884_1.fastq <==
@SRR6575884.1 1/1
CCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTACCGGCGGGAGAATGGT
+
-8F-FFFF-FFFFF8FFF8FF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FF-FF-F-F-FFFFFF-FFFFFFFFF-FFFF-FFFFF----FF
@SRR6575884.2 2/1
GGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGA
+
FFF8-FFF-FFFF-FFFFFFFFFFFF8FFFF8FFF-FFFFFFFFFFF--FFFFFFF-FFFF-FFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575884.3 3/1
GCGCACGAGAGGGGGCATAGAATAAGTAGCGACTTGTAAGACTGTAGCTGCTGCAGCTTCTGTTCCTGTCTCTTCGATGGTCAGCACAGCCTTATGCACA
+
88F8-FFF-FFFFFFFFFFF88F8FFF8FFFFF8FFF8FFF-8FFFFFFF-FFFFFF-FFFFFF-F-F--FF--FFF-FFFFFFFFFFFFF-F--FFFF-
@SRR6575884.4 4/1
CTTCTGACTGCGCCCTGAGGACGTGGACGCTGTTAGGAACCAAACTCTGTCCTGAGCTTCCTCTAGCTCACTCTAGAAGTAATGGTCTAATCAAAGGTCG
+
8FF-F-FFFFFFFFFFFFFFFFFFFFFFFF8F8FFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFFFFF
@SRR6575884.5 5/1
ATTTTAGCCCATGGTTTCAGGGTATAGTCCATAATGGCAGGGAAGTCAAGACATCAGCGTGAGCAGCTGATCATAATGCACGTGTGGTGGTTGCTCCACT
+
F-FFFFFFF-FFFFFFFF8FFFFFFFFFF8FFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

==> SRR6575884_2.fastq <==
@SRR6575884.1 1/2
AGTTGCGGCACGCCGACCCCACGGCGGACGCGTAACAAGTAAGCATGCCAGAGTCTCCTTCTTAATCGGAAGTAACCAGACAAAACCCTCCACCAACTAA
+
FFF-F---FFF-F8FFF-FF8FF8--F-FFFFFFFF--F-F--FFF-F-F-F-FF-F--F----F-F-FFF--FFFF-FFFFFF-F-FFFFFFF-FF--8
@SRR6575884.2 2/2
TATGTGAGGAGCATGGAATCCTTAGAGAATATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGACCGAGAATGAAGAATGGCCTGAGCCTCCAG
+
FFFFFF-FFFF-FFFF8F-F8FFFF---F-FFF-FFF-FFF-FFFF-F-FF--FFFFFFFFFFF-FF-F-FFFFF-F--FF-F--FFFFFFF--FF-FFF
@SRR6575884.3 3/2
ATCCTGAGAACACTGAGGAAGCTGAGTTCCATGTGGACGCTTCCACAACATTGAAGGTGCCCATGATGACACTATCGGGCATGCTATATGTGAATCAATG
+
8-FFF-FFFF8F8FF-8FFFFFFFFFFFFFF--FFFFFF-FFFFFF-FFF-FF-FFFF-FF-FF-FFFF--F----FF-8FF-FF--FFFFF-FF-F---
@SRR6575884.4 4/2
ATCCTAATCAGAGTGCTCAATTTTGTTGAAGGTGCTCAAGGCTCAAACTTCAAAAAGGTCAACTGGGCTAGTTAGTGAAACCATTGGGTGTGCTGGCTAA
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFFF-FF-FFFFFFF8FF8-F
@SRR6575884.5 5/2
AGTCACTACAGTCTGCATTAATTCTCTTATCTGTCACGTGTTAGTAGGGGGTATGCAGAGACATGACCAGCTCTCACAGGCTAATGTTAATTGTCAACTT
+
8FF-FFFFFFFFFFFFFFFFFFF8FFFFFFFF-F-FFFFFFFFF-FFF-FF-F--FFFF-F-FF-FFFFFFFFFFF---FFFFFFFFFFFF-FFFF-FFF

Starting FASTQC command


Processing SRR6575884_1.fastq

Printing command:
fastqc --outdir SRR6575884_1.fastq

Analysis complete for SRR6575884_1.fastq

Processing SRR6575884_2.fastq

Printing command:
fastqc --outdir SRR6575884_2.fastq

Analysis complete for SRR6575884_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 261M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 25 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:46 SRR6575884_1.fastq
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:46 SRR6575884_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:32 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================