-----------------------
Start of variable list:
-----------------------
Sample_ID:
N11-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-pe2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791288
Current job name : Step_02_N11-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/8791288.1.p

Loading required modules...


List files in scratch directory:

total 39M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 22 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 N11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:46 SRR6576780_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:46 SRR6576780_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576780_1.fastq <==
@SRR6576780.1 1/1
GTATCAACGCAGAGTGCATGGGAGTGAGTGTACGCTCGATCGGCCAGACCCCACGGCGTCGCCATGTTGGGCATGATCAGGAACTCACTGTTCGGGAGCG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576780.2 2/1
GCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576780.3 3/1
GTGCTATGTGGGGATCTCAATGTGGCTCATGAAGAAATTGACCTCCGTAACCCCAAAGGAAACAAAAAGAATGCTGGCTTTACTCCCCAGGAGCGCCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576780.4 4/1
CGTCATCTCTGTGCAACACAATGAAGACATCACACTGGAGGCCATGCAAGAGGCCCTGAAAGAGCAGGTGATCAAAGCTGTGGTGCCAGCCAAGTACCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576780.5 5/1
GTGCAACAAATCATGAAGTTTAAGTCTGTAGATGATGTGATCAAGAGAGCAAACAATACTACCTATGGTTTAGCAGCAGGACTCTTCACTAAAGACCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576780_2.fastq <==
@SRR6576780.1 1/2
GTCATACCCATGCCGACTCCTTTGTCATTGGTGCCACCCACATACTTCATGATCTTGGGCATCGCTTCCCGGAGAGCCTCATCCACTGGCTTGTCTGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576780.2 2/2
GTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGTGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF8F
@SRR6576780.3 3/2
GCTAGGTAAAGGGTGATGGGACAGTGGTCACTGCCAAGAGCCTTGGACCGGATCTTGCTGTCACACAATGCAGGTAAAAGAGAGTGGGAAAGCAAAAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-F-FFFFFFFF-FF88
@SRR6576780.4 4/2
TTGCTGGATAGGGGAAAATTAGAAGAAGCTGGCTTTGCCCTGAGGGTAGAAGGCAAGGAGGGCACTCTGGGAGAGGCTAGGAGACCAGGGAGTTGAGATC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF--F-F8F
@SRR6576780.5 5/2
GATAAGAACTGGGGTCACATATTAGAAGGTGAATGAATCTGTTGGATTAAGCCACATGTTTTTTATGAGTGACAGTAACACTGATGAATTCATTTTGCTT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--F

Starting FASTQC command


Processing SRR6576780_1.fastq

Printing command:
fastqc --outdir SRR6576780_1.fastq

Analysis complete for SRR6576780_1.fastq

Processing SRR6576780_2.fastq

Printing command:
fastqc --outdir SRR6576780_2.fastq

Analysis complete for SRR6576780_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 200M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 22 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 N11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 100M Oct 12 19:46 SRR6576780_1.fastq
-rw-r--r--   1 kkarri waxmanlab 100M Oct 12 19:46 SRR6576780_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:24 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================