-----------------------
Start of variable list:
-----------------------
Sample_ID:
A3-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-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790929
Current job name : Step_02_A3-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/8790929.1.linga

Loading required modules...


List files in scratch directory:

total 53M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:42 SRR6575727_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:42 SRR6575727_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575727_1.fastq <==
@SRR6575727.1 1/1
ANTTCACGGTGGAGCACACCCGCCAGGCCTCGGAGGAGGAACTGTTCTGCTCCTTCCAGCAGCGGCTGCAGTGCATGATGANGGCTGGCACCACGCTGGT
+
-#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575727.2 2/1
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGGGACAAGTGGCGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575727.3 3/1
AAGGAAGGCAGCAGGCGCACAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575727.4 4/1
ATTCCCATACATGCAGTCTGTCTCAGAGTCGCTCGGCCCACTTGGTTCCTGGGAAACTGTGGGCAATTCCACAACACTCCCTCCTGTCTCTGAGCACCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFF-FFF-FFF-FFFFFFFFFFFFFF-FFFF-FFF-FF-FFFF--F-FFFFF-F
@SRR6575727.5 5/1
GATGAAGTAGTTCCTGAATTTAATGTCACTGGTCACTTCATGGGGAAGGCTGTTGGGGATGAGGTCAATGAATCTCTGGACCTCATGAATCATGGCATCA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575727_2.fastq <==
@SRR6575727.1 1/2
NATCTNTGTTGTCAACATGCAGGTCCCCATTTCTGCTGAGTTCCTTCAGCCTTGGCAGGTGGTGACTGATGATGTCATCAGCAGCTTCCACTGCAGTTTT
+
#F-FF#FFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575727.2 2/2
NTATCAACGCAGAGTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575727.3 3/2
NTCCCAAGATCCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575727.4 4/2
NACAAGGGCCCTTGGTGCTACACCACTGACCCGAGCGTCAGGTGGGAATACTGCAACCTGAAGCGGTGCTCAGAGACAGGAGGGAGTGTTGTGGAATTGC
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575727.5 5/2
GGACAGGAGCCGCATGCCCTATACTGATGCCATGATTCATGAGGTCCAGAGATTCATTGACCTCATCCCCAACAGCCTTCCCCATGAAGTGACCAGTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575727_1.fastq

Printing command:
fastqc --outdir SRR6575727_1.fastq

Analysis complete for SRR6575727_1.fastq

Processing SRR6575727_2.fastq

Printing command:
fastqc --outdir SRR6575727_2.fastq

Analysis complete for SRR6575727_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 302M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 151M Oct 12 19:42 SRR6575727_1.fastq
-rw-r--r--   1 kkarri waxmanlab 151M Oct 12 19:42 SRR6575727_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:39 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================