-----------------------
Start of variable list:
-----------------------
Sample_ID:
D8-MAA100140-3_57_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 19:44:30 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791092
Current job name : Step_02_D8-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791092.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:44 SRR6576030_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:44 SRR6576030_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576030_1.fastq <==
@SRR6576030.1 1/1
GNCCCGATGACCAGAAAAATGGTCCTGCCAAGCGGCTACAGTGTTCTTCTTTCAGATACAGTAGGATTTATTCAGGATCTTCCGACGACATTGATTGCTG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576030.2 2/1
TACCATTGTTCTACAGGCTTTGGAATTGATGGACCAGCATTTATTATATGCGAAGGAGGAAAGTGGTCTGACCCACCAAAATGCATAAAAACGGATTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576030.3 3/1
CTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGAGCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFF-FF--FFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576030.4 4/1
GTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCC
+
FF-8FFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFF8FFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576030.5 5/1
GTGTATATGAGTTCAGGGACAAGCTATGTGGACCATATGAGAAATTCATATGTGAGCAGGAACATGAGAAGTTCTTGAGGCTTCTAACAGAGACGGAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576030_2.fastq <==
@SRR6576030.1 1/2
NTTCTNTTACTTCCTCAAGCGTTGAGCGGAATGCAGCAATCAATGTCGTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576030.2 2/2
NGAATTATCTTTGCATACTGGCTGTCCAATCCACCGACTATTAACACATGTCACAGTGTCTGAGCCATTCATTTGATAAGGAGATTGACATCTGAATGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8FFFFFFFFFFFFFF-FFFFF
@SRR6576030.3 3/2
NTTTTTAACTGCAGCAACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8FFFFFFFFFFF8FFF-FFFF
@SRR6576030.4 4/2
AGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFF-FFFFFFF-8FFFF8FFFFFFFFFFFF-FF
@SRR6576030.5 5/2
ATCCTTGCCTCTGAAGTCCGCTGCAATCTTGGCATAGTGCTGCAGGCGCTGCCCCAGCTCCTCCAACACTTTCGGTCGTTCCTCAGCTTCTTGAACTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-8F8F

Starting FASTQC command


Processing SRR6576030_1.fastq

Printing command:
fastqc --outdir SRR6576030_1.fastq

Analysis complete for SRR6576030_1.fastq

Processing SRR6576030_2.fastq

Printing command:
fastqc --outdir SRR6576030_2.fastq

Analysis complete for SRR6576030_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 322M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:44 SRR6576030_1.fastq
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:44 SRR6576030_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:08 EDT 2018
0 hours, 0 minutes and 38 seconds elapsed.
==========================================================