-----------------------
Start of variable list:
-----------------------
Sample_ID:
F1-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 19:44:29 EDT 2018
Running on node : scc-ya3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791149
Current job name : Step_02_F1-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/8791149.1.y

Loading required modules...


List files in scratch directory:

total 94M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 31 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:44 SRR6576068_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:44 SRR6576068_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576068_1.fastq <==
@SRR6576068.1 1/1
CTGTGTGGATATCTTACATTCTGAGAAGCCCATGAAGCTGTTCGTAAGTATGAGAATACTGGGTTCTCGTGGCTCGAAGTGACCATCCAGAAGCCTCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576068.2 2/1
GATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576068.3 3/1
CCAGAAACTTCTCCACCAGCTTCAGGTCATTGTTGACAAAGAGGCCATTGCCTGTGCTCAGCTGCAGCTCACTGTCTGGTCTGTTGAGGGTTTGGAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF--F-FFFFFF-FFFFFFFFF
@SRR6576068.4 4/1
GGACCGCCCACGCTTTATCGGTGTTGGGTTAAGCACCGCCCGGACAGCCTCCGCAAACACCTCCTTGACGCCGTCTTGTTGCAGTGCTGAGCACTCGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576068.5 5/1
TAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAATGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576068_2.fastq <==
@SRR6576068.1 1/2
NTGTCATTCAAAAGCAGCATTAGTCCTCTCTGAGGGTCATCCAGGGACAGGAGGCCGATGGTGACTTTGTCTGGGCCACTGAGCTGTAGGAGTCCCATCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576068.2 2/2
CCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576068.3 3/2
GTTCCCAGCTTTCTGGCTGAGGATGTTCAGGAGACAGACACCTCCCAGAAGGATCAGTCCCCAGCCTCCCATGAGATCGCTACAAACCTGGGAGACTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8
@SRR6576068.4 4/2
GAGTGCGGTTGATGGGCGCACCGTGAACCTAAACCTGTGGGACACTGCGGGCCAGGAGGAATATGACCGCCTCCGCACCCTTTCCTACCCTCAGACCAAC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF--FFFFF8FFFFFFFF
@SRR6576068.5 5/2
CTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576068_1.fastq

Printing command:
fastqc --outdir SRR6576068_1.fastq

Analysis complete for SRR6576068_1.fastq

Processing SRR6576068_2.fastq

Printing command:
fastqc --outdir SRR6576068_2.fastq

Analysis complete for SRR6576068_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 505M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 31 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 253M Oct 12 19:44 SRR6576068_1.fastq
-rw-r--r--   1 kkarri waxmanlab 253M Oct 12 19:44 SRR6576068_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:52 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================