-----------------------
Start of variable list:
-----------------------
Sample_ID:
E7-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-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791128
Current job name : Step_02_E7-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/8791128.1.linga

Loading required modules...


List files in scratch directory:

total 95M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:44 SRR6576055_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:44 SRR6576055_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576055_1.fastq <==
@SRR6576055.1 1/1
GTTTTGTTTTCTTCTGATTTCTGACACCAACCTGTTTTGCTAGAAGTTTTGGGCATGAAGTCATTGTTGAGGATAATCATTGCAAAGGCATCCCTGGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.2 2/1
GNACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576055.3 3/1
CNCCCGTTCCTATCTGAGAGGACCACTTCTTCCTGAAGCTGGAACCCGATACTTGTTGGTGCCAACAACTGAAACCAGCAGGAAAAGAGGGTGTGTGAGC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.4 4/1
GNAATGAAGAGCCGGGCCGCCCTGGCCTGGCGCCTGGGAACACAGGGGCAGGTGGGTATAGAAGTCACCGGCTGTGAGCTGNAGGCCCTGGGCAGTGGAT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576055.5 5/1
TTTAGGCACTGTGCTGAATTATTACAAGGGCTTATGGAAATTTGACATGGAGTGCTATGAAAAGTATGGAAAAACATGGGGGTTGTTTGATGGTCAAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576055_2.fastq <==
@SRR6576055.1 1/2
NAGAACATACTCCCCAGGCTCTTGGAGCTCTGGTTCTTGGGTTGCTGGAGAGAACCCTGAGTCTCTTGGTCACTCCTCACATGTGCCTTACCTCCAAAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.2 2/2
NAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.3 3/2
NTGCTNGACTGAGTCCTCGGTGCCAAAGAATATTGTTCAATATTTGCTGAGTGAACAATACTGAGGTTGACTTCTGGCCTCCAAATGGACACACGTGCTC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.4 4/2
NTTCTNAAAAGAGNTCTAATAGAGAAAATATACAAAGCATTTAAGGGCTCCACTACCATGGAGCACCCAAGTCTGACCCGAGGCACCAAAGCCTCTCCCA
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576055.5 5/2
TTATCCCCACTGGGCCAAATTCCCGCCGGTTTGTGAAGACAGAAAAACATTCCTTCACTAGAACATTCTTAATCATCTCTGGGTCCGTGATGACAAAGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-8FFF

Starting FASTQC command


Processing SRR6576055_1.fastq

Printing command:
fastqc --outdir SRR6576055_1.fastq

Analysis complete for SRR6576055_1.fastq

Processing SRR6576055_2.fastq

Printing command:
fastqc --outdir SRR6576055_2.fastq

Analysis complete for SRR6576055_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 518M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:44 SRR6576055_1.fastq
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:44 SRR6576055_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:21 EDT 2018
0 hours, 0 minutes and 51 seconds elapsed.
==========================================================