-----------------------
Start of variable list:
-----------------------
Sample_ID:
E6-MAA100140-3_57_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 19:44:30 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791125
Current job name : Step_02_E6-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791125.1.linga

Loading required modules...


List files in scratch directory:

total 78M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:44 SRR6576053_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:44 SRR6576053_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576053_1.fastq <==
@SRR6576053.1 1/1
GNATGAAGTGCTCCAGTATGCAGAAGTTTGGAGAGAGAGCTTTTAAAGCATGGGCAGTAGCTCGTCTGAGCCAGACATTCCNCAATGCTGACTTTGCAGA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFF-FF
@SRR6576053.2 2/1
ATACATAAGTGTATAATGTCTCGGACCCGTCGCAACGGTTGTTAATATGACAGGCCGCTAAAGACGTTCTACTCCGCCATATGAGATAATATCCTTATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576053.3 3/1
ANGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATGTCAGCAAAACTTTTTTTTGGGAAAGAAAAAATAAAATTGGACAGGTGGGGGGGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--8FF-F-F---F-F---F-FF-F---------F-FF---FF-----------FFF-F--
@SRR6576053.4 4/1
CTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576053.5 5/1
GTATATTCAATATCCCTGTGGGATATTCTGACCATACATTGGGAATACTCGCCCCAGTAGTTTCTGTTGCCTTAGGAGCGGATGTTATTGAGAAGCACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

==> SRR6576053_2.fastq <==
@SRR6576053.1 1/2
NACTANGACAGTGGGCTTTCTTCAACAGTGGTTTATCGCAGCAAGTCTGCAGTTTGCTGGAGATAGTCGCCTGGTTTTCACACATGTACTTGGCAAGTTC
+
#8FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576053.2 2/2
NTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTCGTCAACCCCGGCGCTGTTCCAAGTTGGTACAGAACTGAGTGTCATGTGTACAATGTTAAGCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F--FFFFFFF------FF--F--FF----F-FF-FF-F--F-FF-F-F-FFF--FFFF--F
@SRR6576053.3 3/2
NGCAGGCAATTCAAACAATGCAGAGTGAATTTTTTTACCTTACCACCAACTTGATAAACGACACAATAGAGCTTCGGGAGTCTCAAACAATAGGTGACCA
+
#FFFFFFFFFFFFF8FFFFFF8F8FFFFFFFFFFFFFF-FFFF-F--FFFFFFFFFFFF-FFFFFFFFFFF-FFF---FFF-F-F--FFFFFFFFFFF-F
@SRR6576053.4 4/2
NAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576053.5 5/2
NTCTTGCTTCAACAATAACGTCTCTTTCAGAAGGCATTGGTATCTTTTCCCCACTTCCAAGCATTTTTTCAACTAATCTTATGTTATTAACCATTTCCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6576053_1.fastq

Printing command:
fastqc --outdir SRR6576053_1.fastq

Analysis complete for SRR6576053_1.fastq

Processing SRR6576053_2.fastq

Printing command:
fastqc --outdir SRR6576053_2.fastq

Analysis complete for SRR6576053_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 426M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576053_1.fastq
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576053_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:13 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================