-----------------------
Start of variable list:
-----------------------
Sample_ID:
B3-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 19:41:27 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790729
Current job name : Step_02_B3-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/8790729.1.linga

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6575970_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6575970_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575970_1.fastq <==
@SRR6575970.1 1/1
GTATAGCCCAGGCAGGTAGTTTCCGAACACCACCACCTGTGTGCTGATCCTTGCGTTCCACGAAGCCCTTGGTCTGCCTATCGTGTTGTGACCCACACTG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575970.2 2/1
TGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTT
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575970.3 3/1
GATATATTTTTACAATCCTGCAAACTTCCTTGAGTCACTCACGACTCCCCCTGAGGTCACTTCCTGGTAGTGTCCCAATGCTCTGTGTGCAGTTACTTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575970.4 4/1
TGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575970.5 5/1
GATATATTTTTACAATCCTGCAAACTTCCTTGAGTCACTCACGACTCCCCCTGAGGTCACTTCCTGGTAGTGTCCCAATGCTCTGTGTGCAGTTACTTCA
+
FF-FFFFFFFFFFFFFFF8FFFFFFFFFFF8FFF8FFF8FFFFFFFFFFFF-FFFFFFFFFFFFF-FFF-FF-FFFFFFFFFF-FFFFFF-FFFFFFFFF

==> SRR6575970_2.fastq <==
@SRR6575970.1 1/2
NGCTGGGACATTACTGATACAGACACCATCACTGGGCAGCACGTGGTACACAAGCCACAGCCACACAGGTTGAGCTACCCACGTGGTCCATGCAATACTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575970.2 2/2
GAACTGAGGCCATGAGTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575970.3 3/2
ATATAGACATCCATTGTATGGCTTCAAAAAGTAAAGGGGGCGGGAGCCTAGCTCAGTGGTCACACTTGCCTGGCGTGTAAGGCACTGGGTTGGATCCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575970.4 4/2
GAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575970.5 5/2
ATATAGACATCCATTGTATGGCTTCAAAAAGTAAAGGGGGCGGGAGCCTAGCTCAGTGGTCACACTTGCCTGGCGTGTAAGGCACTGGGTTGGATCCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575970_1.fastq

Printing command:
fastqc --outdir SRR6575970_1.fastq

Analysis complete for SRR6575970_1.fastq

Processing SRR6575970_2.fastq

Printing command:
fastqc --outdir SRR6575970_2.fastq

Analysis complete for SRR6575970_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 168M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6575970_1.fastq
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6575970_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:55 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================