-----------------------
Start of variable list:
-----------------------
Sample_ID:
F5-MAA100040-3_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 19:46:08 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791164
Current job name : Step_02_F5-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791164.1.linga

Loading required modules...


List files in scratch directory:

total 42M
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 F5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:46 SRR6575233_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:46 SRR6575233_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575233_1.fastq <==
@SRR6575233.1 1/1
ANGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCTGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATA
+
F#F--FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF8FFF8FFFF-FFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--F-FF
@SRR6575233.2 2/1
CTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575233.3 3/1
GCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCC
+
F-FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575233.4 4/1
CATCTACAGTGTCAGGGTGATTTTGGAGGCCATTCTGCTGTTCTAGGAGCTGAAAGGTGGGAATGCATAGCGCCTGGAGCATGTCTAATAACCCCTGCCG
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575233.5 5/1
CGATCCATCGCGTATAGGGACGCCCCCTGCTCGCGTTACTGCCAAGCGAGCGTGGTGTGGTGCCCCCGACCTACAACTTGCGCCAATTATCGAGCTGGTA
+
FF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575233_2.fastq <==
@SRR6575233.1 1/2
NTCCANTTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGG
+
#FFFF#F-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8
@SRR6575233.2 2/2
TTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575233.3 3/2
GCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575233.4 4/2
GTTCAGGTTATGGCATTGAAAAAGCTGTTGTCTCAGGAGCCCAGCAATGGCATTTCTTCAGATCCCACTGTCTTCTTAGATCGCCTGGCAGTAATATTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFF
@SRR6575233.5 5/2
GTTAACAAGACGGCGCAGGTTGATGCTTCCAATAAACATGATCTTTCTGCTCCGCTGAGAAGTACACCTTTTTGCTAGCATCTCGCACGGCAAGAGCGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-

Starting FASTQC command


Processing SRR6575233_1.fastq

Printing command:
fastqc --outdir SRR6575233_1.fastq

Analysis complete for SRR6575233_1.fastq

Processing SRR6575233_2.fastq

Printing command:
fastqc --outdir SRR6575233_2.fastq

Analysis complete for SRR6575233_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 239M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 119M Oct 12 19:46 SRR6575233_1.fastq
-rw-r--r--   1 kkarri waxmanlab 119M Oct 12 19:46 SRR6575233_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:28 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================