-----------------------
Start of variable list:
-----------------------
Sample_ID:
O3-MAA000907-3_11_M-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 19:49:49 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791355
Current job name : Step_02_O3-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791355.1.linga

Loading required modules...


List files in scratch directory:

total 13M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 33 root   root      112K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 O3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 6.6M Oct 12 19:49 SRR6576692_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 6.4M Oct 12 19:49 SRR6576692_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576692_1.fastq <==
@SRR6576692.1 1/1
GGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAAC
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-F-FFFFFFFFFF-FFFFFFFFFF
@SRR6576692.2 2/1
ATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAGGTGCACTTTTAGGAGATGACCA
+
FFFF-FFF-FF-FF8F-FF8F8FFFF8FFFFFF8FFFFFFFFFFFFFFFFFFF-FF-F-FFF-FFFFF--FFFFFFFFFF-FFF-FFFF-FF-FFFF-FF
@SRR6576692.3 3/1
TATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATACATACTATGTAGTAGCCCATTTCCACTATGT
+
-F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--FFFFFFFFF
@SRR6576692.4 4/1
ATCCAATGGTCCCCAGAACTTGTAGTCTGTACCAGGAATGCCTGTTCCTCCTGAGAGGTCACCGAAGCCAGGTGCGCTCCCTGGGACGTACAGACCTTCT
+
FF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFF-FFFFFF-FFFFFFFFFFFF-FFFFF-FF-FFFF--FF-F
@SRR6576692.5 5/1
CCCCTGGACTGTGGTGTCCAGTGCATATCTGGCCACCATGGGGGCTCTGGAGCCCTCCTGGTGCCTTCTGTTCCTTCCTGTCCTCCAGACTGTGGGAGGA
+
F8--F-FFFFFF--FFFFFFFFFFFFF8FF8FFFFF8FFFFFFFFFFFFF--F-FFFFF--F-F--FFFFF--FFF----FFF-F--F-F-F-FFFFFF-

==> SRR6576692_2.fastq <==
@SRR6576692.1 1/2
GAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576692.2 2/2
GTTTGATACTGTGTTATGGCTGGGGTTTTCATGTTGATAATAGTGGTAATAAAATTAATTGCACCTAAAATAGATGACAATACAGCTAAATGAAGGGAGA
+
FFFFFFFFF8FFFFFFFFFFF8-8F--FFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFF-FF-FFFFFFFFFFF-FFF-F-FF-FFFFFF-FF-F-F--
@SRR6576692.3 3/2
GGTGTAAGCATCAGGGTAGTCTGAGTAGCGTCGTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAATGTTATGTTTACTCCTACGAATATGATG
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFF-F-FFFFF--FFFFFF-FF-FFFFFFF---FF-FFFFF-FFF
@SRR6576692.4 4/2
CATCTAGAGGATGTGAATGCTGACATCCTGCAGACAAAAGATGTGCTGTAGGAATCTGGAGCCGTGGCTTTGGAGACCCAGGCGCTGAGAAGCTCCTTGG
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF--FFF--FFF-FFFFFFFFFF-FFFFF-FFFFFFFFF-FFFFFFFFF-F--FFFFFFF
@SRR6576692.5 5/2
GCCAGGGCAATCAGCAGAGTCAACACCAAGTCACCCAGAACAATCCCAGCCAGTACACCAGGGCTCACGGAAGAACAGTCGCATCTTGGGAAAGTGTCAC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

Starting FASTQC command


Processing SRR6576692_1.fastq

Printing command:
fastqc --outdir SRR6576692_1.fastq

Analysis complete for SRR6576692_1.fastq

Processing SRR6576692_2.fastq

Printing command:
fastqc --outdir SRR6576692_2.fastq

Analysis complete for SRR6576692_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 70M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 33 root   root      112K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 O3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:49 SRR6576692_1.fastq
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:49 SRR6576692_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:06 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================