-----------------------
Start of variable list:
-----------------------
Sample_ID:
H9-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 19:41:27 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790805
Current job name : Step_02_H9-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/8790805.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 45 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 H9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576404_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576404_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576404_1.fastq <==
@SRR6576404.1 1/1
GATCCCAAGAATACTCACATCTTCATCAGCTGGATGATTGCACAGTCTGTCACTGCTGTCGCTGGCCTGACTTCCTATCCTTTTGACACGGTTCGCCGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF
@SRR6576404.2 2/1
GAAATAAGTTAGCTCTAAAGTTAACCATGATGAAAGAGTCTATCTTCCATGGCTTCCAAGTCTGCTAATATCTGGAATAACTGCACAGTAACTGTGCGTA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576404.3 3/1
TGTTGAAGAAGAAACAGTACACATCCATCCATCATGGCGTGGTGGAGGTCGACGCCGCCGTGACCCCAGAGGAGCGCCATCTCTCCAAGAAGCAGCAGAA
+
FF8--FFFFFFFFFFF-FFFFFFFFFFFFFF8FFF-8FFF--FF-F-FFF-F-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFF
@SRR6576404.4 4/1
GCCTTCCTGAGCTCCCTGACGGATGTTCGCCAGGCCCTGGCAGCACCTCGCCTAGCGGGGAAGGAGGGCCCCAGCCTGGCTGAGTTGCTGGCCAATGTGG
+
F8F8FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576404.5 5/1
ACTATGACAATGTTGATCTAATTATTTTCGTCCAGAATCAAGTAACTTCCTATGAGTTCTTTTTCTTGTTGCTTTTAGAGTCCAGTTTTGAGCCAGCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF

==> SRR6576404_2.fastq <==
@SRR6576404.1 1/2
ATATTATACAACATGCCTGTTCTCGGGGAGAACACCTAGGACATAATTATGTGTATTTCTTGATCTCATCATACAAGACAAGCACAAAGGCGCCACCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFF-FFFFFFFF-FF
@SRR6576404.2 2/2
ATCTTATAGTGCCAGCTACAGCAAGGGTCAGTGAACTGCAAGGAAAGTACATTACTTCCTGTACTGGTAAACGTCTAGCTCCTCACATGGAGAGAAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8FFFFFFFFFFF8FFFFFFFF
@SRR6576404.3 3/2
GAATGTAAAGAGAGAAAGCGAGAATACATAACTGATTTGTAAATTAATTCAAGTTCAGGCATCTACTTGTGATACAGCACACCTGTCAAAATCCGAGGGT
+
FFF---FF-8FFFFF-F--8F8FFFFFFF-F--FF--F--FFF-FFFF-FFF--FFFFFFFFF-FFF--FFFFF-F-FFFFFFF----FF---F-F--F8
@SRR6576404.4 4/2
CCCCTGAAGTAGGACTTATTGGAGAAGGACACCTCCTTGGCGGTAAAGAGATGCACAGAAGCCAGTGACGTCTTGATGTGGCTTAGGATGGATCTGGCCA
+
F-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576404.5 5/2
GAACAGCAAAAAAAGATAAGCCAGAAAAATGACCATGCAAAGTCACATTGGATACCAGAGTCCTGAGGGATGGATGGGTTCAGGGGGAAAAAGCAGAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576404_1.fastq

Printing command:
fastqc --outdir SRR6576404_1.fastq

Analysis complete for SRR6576404_1.fastq

Processing SRR6576404_2.fastq

Printing command:
fastqc --outdir SRR6576404_2.fastq

Analysis complete for SRR6576404_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 107M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 45 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 H9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:41 SRR6576404_1.fastq
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:41 SRR6576404_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================