-----------------------
Start of variable list:
-----------------------
Sample_ID:
N5-MAA000907-3_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 19:42:17 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790877
Current job name : Step_02_N5-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790877.1.linga

Loading required modules...


List files in scratch directory:

total 34M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6576648_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:42 SRR6576648_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576648_1.fastq <==
@SRR6576648.1 1/1
GGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGT
+
8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576648.2 2/1
ATATATACCTCGGAGTAAAATGGTTGAGTAGTGTTTTTTGTTGATGTTTTGTTTTGGAGGTAGGAGACAGCCCCTCCTCTCTGATTTTGATTCAGGTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576648.3 3/1
GCATTAAATGAAGAGAACAAGATGCACAGATACATGCAGTGCAACTCAAGCTAGGACTCTGAGAGAGAAAATGATGAGTAGATATTTAAAGTGTAATCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576648.4 4/1
GCCTGAGATAACTCACCACTGTCCAAAGACTCCTTTCTTGCTTGTTGGGACCCAAATTGATCTCAGAGATGACCCCTCTACTATTGAGAAACTTGCCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576648.5 5/1
ATACAGAGCTGAGCCAACCAAAGGCAAATCCAAAGACTCCGGCGTAGACACAGAACCCAACGTAGGTTGTAGACAAAGGGGCAAGCAAATGGCACACTCC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576648_2.fastq <==
@SRR6576648.1 1/2
GCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576648.2 2/2
CATCTAGGGACGGCTATTTTGTTTCTTTACTGCGCCCATTTTCATTCACTATTTAAAATATTAAATTAAAAAGCCAGATATGGTGACTATGCTGAGCCTG
+
FFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFF--FFF-FFFFFF8FFFFFFFFFFF8FFF
@SRR6576648.3 3/2
GATAATCAGACCAGGAAGTGAAAATGACATTCAAACTAAATTATTTAAAACAAGGCATACCTCTCCCCAACTCAGTCTAAAGACACAATTTCATTTAGAG
+
FFFFFFF-FFFFF8FFF-FFFFFFFFFFFF--FFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF-FFF-FFF-FFFF-8F-FF-FFF
@SRR6576648.4 4/2
ACTCTCCAAAATGGAACCAGGGAGCAGCTTTGACAATCTGAATTAGTCTGTTACAGTCAATACAAGCATGCTTGCTTTTAAACAAAAAAACAACAAACGT
+
FFFFFFFF-FFFFFFFFFFFFFFF--FF-FFFF-FFFF-FFFFFFFFFFFFFF-FFFFFFFFFFF-FF-FFFFFFFF-FFFFFFFFFFF-F-FFFFF--F
@SRR6576648.5 5/2
ATACAGATCTCATTGGAGGAAGTCCCAAAGGAGAAAAGCTGTCCGTCTTCCAAACAATTAACAAATTCCTGGACTTGTCGCTGTTTACCCATAGGGGCTT
+
FFFFFFFFFFFFF8FFFFFFF8F8FFFFFFFFFFFFF-FFFFFF-F-FF-FFFFFFFF-FF-FFFFFF-FFFFFFFFFF-FF-FFFFF--F-----888F

Starting FASTQC command


Processing SRR6576648_1.fastq

Printing command:
fastqc --outdir SRR6576648_1.fastq

Analysis complete for SRR6576648_1.fastq

Processing SRR6576648_2.fastq

Printing command:
fastqc --outdir SRR6576648_2.fastq

Analysis complete for SRR6576648_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 177M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  89M Oct 12 19:42 SRR6576648_1.fastq
-rw-r--r--   1 kkarri waxmanlab  89M Oct 12 19:42 SRR6576648_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================