-----------------------
Start of variable list:
-----------------------
Sample_ID:
J17-MAA000377-3_9_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 19:46:09 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791265
Current job name : Step_02_J17-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791265.1.linga

Loading required modules...


List files in scratch directory:

total 47M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 J17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:46 SRR6576403_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:46 SRR6576403_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576403_1.fastq <==
@SRR6576403.1 1/1
GNACAGGGCTTTCTGGAGGGAGTTGGTGGAATGCTTCCAAAAGATATCCAAAGACTCGGACTGCCGGGCTGTTGTAGTCTCCGGTGCAGGAAAGATGTTC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576403.2 2/1
ANATTGGAGAGTGTTGGGGAGGTGGGGAATATGCCACAGCCACAGCCACGATCATGTTGATGGGGGACACATGCACAAGAGGTTGCAGATTTTGTTCCGT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576403.3 3/1
GCACCTGGTCCTTCGCCTCAGAGGTGGCATGCAGATCTTTGTGAAGACCCTGACAGGCAAGACCATCACCCAGGAGGTCGAGCCCAGTGACACCATAGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF---F-FFFF-FFFF-F--FF-FFF-
@SRR6576403.4 4/1
AACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---FFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576403.5 5/1
CACAGGGGCTTTCAGGTGTCTCGTTGAGAAAGGAGATGTAGCCTTTGTGAAACACCAGACTGTCCTGGATAACACCGAAGGAAAGAACCCTGCCGAATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576403_2.fastq <==
@SRR6576403.1 1/2
NGGCTATGCGGGCCGCATCATCTCCTGAGGGCTGCATGAGTTCGGAGGCCATGTCCATGAGGTCAATACCTGAAGTGAACATCTTTCCTGCACCGGAGAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576403.2 2/2
NCACATTGTGTGCATACACATCTAATCCAGACAGAGCCACCTTCTCCACTGCTCTCAGATCACCTCGGAAGTCTGGGGTGAGGCATTCCACGAGGATTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576403.3 3/2
NGGTGATGGTCTTGCCTGTCAGGGTCTTCACAAAGATCTGCATGCCACCTCTGAGGCGAAGGACCAGGTGCAGGGTGGACTCTGACTGCATGGTGTAGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FF-F----F---F----FF----
@SRR6576403.4 4/2
GTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGAAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFF8FFFFFFFFFFFF
@SRR6576403.5 5/2
TCCTCATGTTACCGACAGATTGCATGTACTCCGCTCCTAAGTATTTTTCAGGTGTGGTACCCTCTGGAAGTTTAACGAAACATTTGGTGTCATCCCTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576403_1.fastq

Printing command:
fastqc --outdir SRR6576403_1.fastq

Analysis complete for SRR6576403_1.fastq

Processing SRR6576403_2.fastq

Printing command:
fastqc --outdir SRR6576403_2.fastq

Analysis complete for SRR6576403_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 248M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 J17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 124M Oct 12 19:46 SRR6576403_1.fastq
-rw-r--r--   1 kkarri waxmanlab 124M Oct 12 19:46 SRR6576403_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:30 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================