-----------------------
Start of variable list:
-----------------------
Sample_ID:
G5-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 19:46:08 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791203
Current job name : Step_02_G5-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/8791203.1.linga

Loading required modules...


List files in scratch directory:

total 147M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  70M Oct 12 19:46 SRR6575890_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  77M Oct 12 19:46 SRR6575890_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575890_1.fastq <==
@SRR6575890.1 1/1
GNTTTTCTCTTGGTGTTCTGACTCTGTCCTTGAAGCCAAGGGTCTTGGGGGGGGGGTGCAGTTACCCTCCTAGGGCCCNAGNCCTACCTCCCCTCATCCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6575890.2 2/1
CTGCTTCCCGGCTAACTATGTGCACCTTCTGCCGCACCTGTCCCTCGAAGCGGCCTAGGGACTGCACAAGGAAAGTTGCCCAGCCTACGTGCAGTACTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575890.3 3/1
GCCGTGTGTTGCCGATGAGTCTGCCGCCAACTGTGACAAATCCCTTCACACGCTATTTGGAGATAAGGTGTGTGCCATTCCAAACCTCCGGGAAAACTAT
+
F--F-FF--FFFFF8-F8FFF88FFFF8FFFFFFF-F88F-FFFFFFFFFF-F--FF--FFFFFFFF-F-FFFFF-FFFFFFFFFF-FFFFFFF-F---F
@SRR6575890.4 4/1
ACTGTCAGAGCAGAGAAGCATGGCCGCCTTTCCACCAGGGATCCACTACAGCACTTGGTAACATGCTCACTCACTGGGGTCTTCTCATGCAGCAGACACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575890.5 5/1
GCCCGGGTTAAGGCTGTACTGACTAGCCAGGAGACTTTATTTGGGGGAAGTGACTGCACCGGCAATTTCTGTTTGTTCAAGTCCACCACCAAGGACCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575890_2.fastq <==
@SRR6575890.1 1/2
NTCCTNGAACNGTNTAAACTAGGCTGGCCTCAAACTCAGAAATCCACCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTACACCACCACTGCCTGG
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575890.2 2/2
NAGGATGAGGAGATCTACAAGGAATTCTTTGAAGTGGCCAATGACGTCATCCCCAACCTGCTGAAGGAGGCGGCCAGCCTGCTAGAAACAGGCGAAGAGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575890.3 3/2
NCTCAGTGCCGGAGCAAGCGGGAGGATTGGCGTCAGCGCAGCACTTATCCATAGTGGCTACATATTTCTTAGCAAGTCAAACCAACAAGGATACCGTGTT
+
#--F--F-FF8F88F-FFFFF8FFFFFFFF--F-F-F--FFF---F-FFF---FF--FF-FFF--F-----F--FF-F--F-F-FFF-FFFF-F-FF-F-
@SRR6575890.4 4/2
CTGTTGCTGAGACTTGCTAAGAAATATGAAGCCACTCTGGAAAAGTGCTGCGCTGAAGCCAATCCTCCCGCATGCTACGGCACAGTGCTTGCTGAATTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF--F8FFFFFFFFFFFFFF8FFFFF
@SRR6575890.5 5/2
GTGGTAAGGCACAGCAGCGAAGACTACACCAGTTAGCCCCAACCCCTCAGGGCATGAAGACCAAGAGAAGCCCATGGGCCACGGGAGGGAGCATCTGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFF-FFFFFF-FFFF-FFFFFFFFFFFFFFF8-FFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575890_1.fastq

Printing command:
fastqc --outdir SRR6575890_1.fastq

Analysis complete for SRR6575890_1.fastq

Processing SRR6575890_2.fastq

Printing command:
fastqc --outdir SRR6575890_2.fastq

Analysis complete for SRR6575890_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 784M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 105 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:47 G5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 392M Oct 12 19:46 SRR6575890_1.fastq
-rw-r--r--    1 kkarri waxmanlab 392M Oct 12 19:46 SRR6575890_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:10 EDT 2018
0 hours, 1 minutes and 2 seconds elapsed.
==========================================================