-----------------------
Start of variable list:
-----------------------
Sample_ID:
N3-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 19:49:49 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791350
Current job name : Step_02_N3-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/8791350.1.linga

Loading required modules...


List files in scratch directory:

total 49M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 N3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:49 SRR6576643_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:49 SRR6576643_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576643_1.fastq <==
@SRR6576643.1 1/1
GTATGCAACGGAGCTTGAGCATTCCCTCTCAGCTCCTGCAGGATTGGGTTTTTTTTAGTTTGTTTGTTTGCTTGTTTGTTTTTGCTTTGTTTTACCTACA
+
8F8FFFFFFFF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576643.2 2/1
ATTCTATCCCAGTAACTGGATCTCTTCCATAGCCCACAAGCAAAACAGCATGATTTGTCAGCTCGAAGGGGTTGAAAGGGTCACTCAACCCAGTGTGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576643.3 3/1
CTAGGACAATGGGCATAAAGCTATGGTTAGATCCACAAATTTCAGAGCATTGGCCATAGAATAACCCTGGTCGGTTTGATGTTACTGTTGCTTGATTTAG
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFF-FFFF-FF-FF-FFFFFFFFFFFFFFFFF
@SRR6576643.4 4/1
CTCCAACATTGCGTCCCTGGATAGCTCCTTCTATTCCGCCCCTACCTATGGCTTCATTCCAGATCGATGGAGACATGCTCACACTTGGAGCCAGTCCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFF-FFFFFFFF-F-FFFFFFF-FFFF-
@SRR6576643.5 5/1
ACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGTGTGCATTTATCAGATCAAAACCAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576643_2.fastq <==
@SRR6576643.1 1/2
NTACATGGGGACGCACAGACTCCGAGCTAAAGGTTGAACTCCACCTCCAGGCAGAATGAGGCTCAGCACAGCAACGCTGCTTCTCCTCCTGGCCAGCTGC
+
#FFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFF-FFFFFF
@SRR6576643.2 2/2
NTGGAAGAAAGCTGCTTTCCCTACACAGCCAAAGATTCTCCATGCAAACCAAGGGAGAATTGCCTCCGTTACTATTCTTCTGACTACTACTATGTGGGTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFFFF-FFFFFFFF
@SRR6576643.3 3/2
TCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACT
+
FFFFFFFFFF8FFFF-FFF8FF-FFFFFFFF-FFFFFFFFFFFFFF-FFFF-FFFF-FF-FFF-FFFFFFFFF-FFF-FFF-FFFFFFFF-8FFFF8FFF
@SRR6576643.4 4/2
GACTATACCTGCTGAGCCCTCTCTGTGGGAATGAAAGGGATTCCTCTAGCTTTCAGGGTGGAGGTTCACTGTGTCAGAAGGCACTGTCAGGCCCAGCATG
+
FFFFFF-FFFFFFFFFFFFFF8FFFF-FF--FF-FFFFFFFFFFFFFFFFF-F-F-FFFFFFFFFFFFF-FFFFFFF-FF-F-FFFFFFFFFFFF88FF8
@SRR6576643.5 5/2
AGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576643_1.fastq

Printing command:
fastqc --outdir SRR6576643_1.fastq

Analysis complete for SRR6576643_1.fastq

Processing SRR6576643_2.fastq

Printing command:
fastqc --outdir SRR6576643_2.fastq

Analysis complete for SRR6576643_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 256M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 N3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:49 SRR6576643_1.fastq
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:49 SRR6576643_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:18 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================