-----------------------
Start of variable list:
-----------------------
Sample_ID:
A1-MAA100138-3_56_F-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 19:42:18 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790920
Current job name : Step_02_A1-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790920.1.linga

Loading required modules...


List files in scratch directory:

total 98M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  47M Oct 12 19:42 SRR6575722_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  51M Oct 12 19:42 SRR6575722_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575722_1.fastq <==
@SRR6575722.1 1/1
GCCCAGAACAATGCTAAAGTGGCTGTCCTGGGAGCTTCTGGGGGCATTGGGCAACCCCTTTCACTCCTGCTGAAGAACAGCCCCCTAGTGAGCCGCCTGA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.2 2/1
CCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.3 3/1
CCACATAGGGCGAGTCTGTCAGTTCAATACCAATCTTGGCCAGCGGCGAGCCCAGTGGCCCCATGCTGAATGGGATGACATACATGGTGCGGCCTTTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.4 4/1
GTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCCTCGTAC
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.5 5/1
GTCTTTGGATGACCAAGCAGATCATTTTGGGGTAGCCATTTGACAAGAATTGTGTTCTTTGCAAGATTCGATGGTCTAGTTCCGGTGTAGCGCCACAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575722_2.fastq <==
@SRR6575722.1 1/2
NTGATGGGGATGGTGGAGTTCACTGGGTTGGCAATGATGCAAACCATGGCTTCAGGACAGTGCTGGGCACAGGCAGCCGTCAGGGTGGCCACAATGGTAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.2 2/2
NTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.3 3/2
NCAATGCTCAGCTGTGCCAGCCGGAGTATATCCACATCTGCGATGGCTCCGAGGAGGAGTACGGGCAGTTGCTGGCCCACATGCAGGAGGAGGGTGTCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575722.4 4/2
GGATGGTGAAGTAAAGTCCTAGTATAATGGTAATTAGTAGGGCTTGATTTATGTGGTTTCGTTTACCTTCTATAAGGCTATGATGAGCTCATGTAATTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-
@SRR6575722.5 5/2
CCCTATGGGTCACTTGCCACTGAAATCTTACAGAAAGAAGTGACTGTCCAGGATCTTCTGAGCCCTGCATCTATCTGGCTGATGAGAAGTGACTTTGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575722_1.fastq

Printing command:
fastqc --outdir SRR6575722_1.fastq

Analysis complete for SRR6575722_1.fastq

Processing SRR6575722_2.fastq

Printing command:
fastqc --outdir SRR6575722_2.fastq

Analysis complete for SRR6575722_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 524M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 262M Oct 12 19:42 SRR6575722_1.fastq
-rw-r--r--    1 kkarri waxmanlab 262M Oct 12 19:42 SRR6575722_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:08 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================