-----------------------
Start of variable list:
-----------------------
Sample_ID:
D2-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 19:44:29 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791072
Current job name : Step_02_D2-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/8791072.1.linga

Loading required modules...


List files in scratch directory:

total 163M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  82M Oct 12 19:44 SRR6576017_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  81M Oct 12 19:44 SRR6576017_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576017_1.fastq <==
@SRR6576017.1 1/1
TNATCAGAGAGACAGTCTCTTCATTTTATATAAACAAAACTGACATGTGCCAAAAAAGACCCCAGAGGACAAACAAACCCTAGTGCTGACACTGAAGACC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFF-FFF-FFFFFFF
@SRR6576017.2 2/1
CGCGCTACACTGACTGGCTCAGCGTGTGCCTACCCTACGCCGGCAGGCGCGGGTAACCCGTTGAACCCCATTCGTGACTGTCTCTTATACACATCTCCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576017.3 3/1
GGCCAGAGCGTAGGAAGGTGTAGAGTAGAGGCTCACGGCTCCTGAGACCCACCTCTGCTCTGTGCTGCTGCGTAGAGCTCTCTCCTTGGGGCCTCCAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576017.4 4/1
GCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGCGTGGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576017.5 5/1
CCTCAGGGCTGCTCCACGCCTGCGAGTGAGGAACCCTCAGTAAAGGCTGAGAATGGCCTGTCCACAGAACCCAGCAGTGCCGCTGCAGCCCAGGAGCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576017_2.fastq <==
@SRR6576017.1 1/2
NGTGTTGGAACAGACTGCTGTCCTGTGTGCTGCAGAGTCTGTCCCTTGTTGGCACTTAGGAAGATCCAGTTTCTCCCCCACTGGAAGTCTGCACTTCTCA
+
#FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576017.2 2/2
NCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCTGTCTCTTATACACATCTGACG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576017.3 3/2
NCCGAATACCCTGACCAAAGATGGGCCCTGTCCCTCAAGCTTGTGCCCTGGAGGCCCCAAGGAGAGAGCTCTACGCAGCAGCACAGAGCAGAGGTGGGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576017.4 4/2
NTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAG
+
#--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFF
@SRR6576017.5 5/2
NTTCTGAATTCTCTTCTGCTCATGGAAGGATAAGATGAAGAGGCTGGTGGCAGATCCTGCATAAGCTCGACATTCCCGAAGAAGCGACTCACAGGCATGG
+
#FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576017_1.fastq

Printing command:
fastqc --outdir SRR6576017_1.fastq

Analysis complete for SRR6576017_1.fastq

Processing SRR6576017_2.fastq

Printing command:
fastqc --outdir SRR6576017_2.fastq

Analysis complete for SRR6576017_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 873M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 111 root   root      116K Oct 12 19:45 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 D2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 437M Oct 12 19:44 SRR6576017_1.fastq
-rw-r--r--    1 kkarri waxmanlab 437M Oct 12 19:44 SRR6576017_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:38 EDT 2018
0 hours, 1 minutes and 9 seconds elapsed.
==========================================================