-----------------------
Start of variable list:
-----------------------
Sample_ID:
M16-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 19:46:12 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791284
Current job name : Step_02_M16-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/8791284.1.linga

Loading required modules...


List files in scratch directory:

total 34M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 125 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 M16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  17M Oct 12 19:46 SRR6576714_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  18M Oct 12 19:46 SRR6576714_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576714_1.fastq <==
@SRR6576714.1 1/1
CNTTGTATCTCAGCACCAAGAACACTATTCTGAAGAAGTATNATGNGCGTNNCNNAGNNNTCTTCCAGGAGATCTATGACAAGAAATACAAGTCCCAGTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF#FFF#FFFF##F##-F###FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576714.2 2/1
GTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGTTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576714.3 3/1
ATTTAATGCCAGTTACTCAGACTCTGGGCTCTTTGGAATTTACACTATTTCCCAGGCTGCAGCTGCTGGAGAGGTTATCAATGCTGCCTACAACCAAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576714.4 4/1
GACTTGCTCTCAACAGCAGTTACTTGGGAAGAGCAAGCGTACTCCAATTGCACAGGCCCTGGCTTCAGCCTCCACTCAGATATTGTCATGCCCTATATTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576714.5 5/1
GTTCTTTCCAGTTTGTTTTTGGCTCCCCAAGCGTCATCTCATGTGGAGAACTTTACACCTAACATAGCTGGTGCCAAGAGATGTCCCAAGGACATGCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576714_2.fastq <==
@SRR6576714.1 1/2
NCCTCGGACTTCATAGCTTGGGCCACCATGTCATCTATGAGCCTGTGTTCATAGCAGATCTTCTGAGCTTCAAACTGGGACTTGTATTTCTTGTCATAGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576714.2 2/2
NGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTTTTGTCAGAGGCCAGGATAATAGTATGCCATTCCCCATTAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576714.3 3/2
GTAGAAGGTGGCATATAAGAACCTGCAGCTAGAGCCTGTGACCCAATTTCACTCAGGAAGCCCTCTGACGTCTCCACAGACATTAGATATCCAGCTTTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576714.4 4/2
CGTAGTTCCTGGTTTCTTCAAACATGAACTCACAGGCAGAAATCGCCAACTCAGCAATTAAGAGCCTTTCCTGTGGAAGCTCTTGCATGAGGTAGTAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF--F-
@SRR6576714.5 5/2
GTGTATATGTATACATCACTACCCTAAGATATAGATCTAGCCCTATGGGTATATATACGCATTATGGCTATATAGAAAAACGATGCCAATACTATCCAAA
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFFF

Starting FASTQC command


Processing SRR6576714_1.fastq

Printing command:
fastqc --outdir SRR6576714_1.fastq

Analysis complete for SRR6576714_1.fastq

Processing SRR6576714_2.fastq

Printing command:
fastqc --outdir SRR6576714_2.fastq

Analysis complete for SRR6576714_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 187M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 M16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  94M Oct 12 19:46 SRR6576714_1.fastq
-rw-r--r--    1 kkarri waxmanlab  94M Oct 12 19:46 SRR6576714_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:39 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================