-----------------------
Start of variable list:
-----------------------
Sample_ID:
B9-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 19:42:19 EDT 2018
Running on node : scc-yb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791000
Current job name : Step_02_B9-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/8791000.1.y

Loading required modules...


List files in scratch directory:

total 76M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:42 SRR6575766_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6575766_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575766_1.fastq <==
@SRR6575766.1 1/1
ANTGTGTGCAGGTAGCCTGCTAGCTTGTTGTCATCCACGTACTCAACAGATTCGGTCTTGCCAAAGCCAGGGACACGGATCTGGACACCAGGGGCATTGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F--FFF
@SRR6575766.2 2/1
ATTATATAAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575766.3 3/1
GGATCCTCGTTAAAGGAATTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAG
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF---FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575766.4 4/1
GAGTACTTGGGAGTGGTGACAATCAACAAGAAGAGGAACCTGGTGGTGTCTGTGGATGTTGGGGCTACCTTTGAGATTGTCCTGCACAGAACATGGAAGG
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFFFF-FF
@SRR6575766.5 5/1
GTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF

==> SRR6575766_2.fastq <==
@SRR6575766.1 1/2
NTACATGGGGAGTAGGCACTGGGCTGTGATGGGGCTGCCTGGCTCCCCATGGCAGCGGGTGCTGTTGCTGTTGGGGCTACTGCTCCCTCCTGCCACCCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575766.2 2/2
NTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGTACAAGGTTTAATC
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575766.3 3/2
ACCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-
@SRR6575766.4 4/2
CTTTAATGAGATCACAGGATGTCTTGACACAGGGACCAGTATGCTCAGGAAGGTGGAGTTAATCTGATGCTCTGCTCTCCTCTCCTCCTTCATAGGCCGT
+
FFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFF-FFFFFFFFFFFF-F-FFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575766.5 5/2
TTATTGCTCAATCTCGGGTGGTTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575766_1.fastq

Printing command:
fastqc --outdir SRR6575766_1.fastq

Analysis complete for SRR6575766_1.fastq

Processing SRR6575766_2.fastq

Printing command:
fastqc --outdir SRR6575766_2.fastq

Analysis complete for SRR6575766_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 404M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 202M Oct 12 19:42 SRR6575766_1.fastq
-rw-r--r--   1 kkarri waxmanlab 202M Oct 12 19:42 SRR6575766_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:39 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================