-----------------------
Start of variable list:
-----------------------
Sample_ID:
L8-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 19:41:28 EDT 2018
Running on node : scc-yc2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790853
Current job name : Step_02_L8-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/8790853.1.y

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6576561_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:41 SRR6576561_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576561_1.fastq <==
@SRR6576561.1 1/1
CAGCAAATATGAATCAGTCATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTCTCTAAGGATGAGAAG
+
FFFFF-FFFFFFFFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFF
@SRR6576561.2 2/1
CAGCAAATATGAATCAGTCATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTCTCTAAGGATGAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF
@SRR6576561.3 3/1
AATATATTGTGGGTACATCAAGTCCCTCTGACAAAACAGGGCAGAAGAGAAAGGACTCTGTTTGAGGCAGTTTCTTCGCTTGCCTGTTTTTTTTTTTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFFFFF-
@SRR6576561.4 4/1
TTACTATACCTTGAGTTTAAAGTCGACTTCCTCTTACATTTCTCCCCTGCTTTGGATCTGCTTTGTGCTTGGCTGCTGAGAGAGCAGCACAGGCTAAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576561.5 5/1
TTACTATACCTTGAGTTTAAAGTCGACTTCCTCTTACATTTCTCCCCTGCTTTGGATCTGCTTTGTGCTTGGCTGCTGAGAGAGCAGCACAGGCTAAGAC
+
FFF-F-FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576561_2.fastq <==
@SRR6576561.1 1/2
NATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAACCAAAATTTTATAAAAATCACGTTTATTTGAAAGATAAATTAACCCGTGGGGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--F-----FFFF---FF---F-FF-------F--F---F-------F-FFF-FF--FFF--
@SRR6576561.2 2/2
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGATCCCAATATTTTATAATAATATCGTTTATGTGAATGGTTAATTAAACGCTGGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---F-F---FFFFF-F--FFF----FFF---F---FF-FF----FF-----8F---
@SRR6576561.3 3/2
CGTCATAATTTATTCTGTTGTATAAAAAAAGTCATCCCAGTAACAAAATGTCTTCTCAGAAGAAGAAATATATTACTTCAGATCATAAATAAACAAACAT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFF--FFFFFFFFFFFFF-FFF
@SRR6576561.4 4/2
GATAAGGAGAGACTGATATTATCAGATACTAACATGGGAGGCATCTCTTCTGATGCAGATGTGGAAAATGGCCCGGTGGAAGAACCAGAAGGAAAGAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576561.5 5/2
GATAAGGAGAGACTGATATTATCAGATACTAACATGGGAGGCATCTCTTCTGATGCAGATGTGGAAAATGGCCCGGTGGAAGAACCAGAAGGAAAGAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576561_1.fastq

Printing command:
fastqc --outdir SRR6576561_1.fastq

Analysis complete for SRR6576561_1.fastq

Processing SRR6576561_2.fastq

Printing command:
fastqc --outdir SRR6576561_2.fastq

Analysis complete for SRR6576561_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 207M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:41 SRR6576561_1.fastq
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:41 SRR6576561_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================