-----------------------
Start of variable list:
-----------------------
Sample_ID:
E5-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 19:49:50 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791369
Current job name : Step_02_E5-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/8791369.1.linga

Loading required modules...


List files in scratch directory:

total 30M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 E5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:49 SRR6576273_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:49 SRR6576273_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576273_1.fastq <==
@SRR6576273.1 1/1
GACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576273.2 2/1
TNAGTGTACAGGCCAGCCCTGGCTGCCTCAACACCTCAACCCCCTCCCAGGGAGACCAAAGCCTTCATACATCAAGTTGGGGGGACAAAAAAAAAGGGAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576273.3 3/1
GTGTTAGGGGTAATATTCATTTAGCCTTCTGAGCTTTCTGGGCAGACTTGGTGACTTTGCCAGCTCCAGCAGCCTTCTTGTCCACAGCTTTGATGACACC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576273.4 4/1
GTATCAACGCAGAGTACATGGGAGTTCAGTAATTGGTCACTAGGCCATGAGGAGATGCTTTTGTGGAGACAGGGGTAAGATCGTGTAAGGGCTTAGGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFF
@SRR6576273.5 5/1
CTGGTGTACACTGCCATAGCCACTAATATGGAGAGAGCTGCAGAAAAAGCCATGACAGTTGAGACCAGAGGGCCACGGCCGGGAGCAGACAGGGCTGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576273_2.fastq <==
@SRR6576273.1 1/2
NTTGGGCGGAATATTAGGCTTCGTTGCTTTGAGGTATGAAGGAAAGGTATTAGGGCTAAAATTAGGATAGATAAGATTAAGACTAGGACACCTCCTAGTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFF-F-FFF-FFFFFFFFFFF-FFFF--FFFFFFFFF--FFF
@SRR6576273.2 2/2
NCCAAAAGCCACCCCCACTCCTAAGAGGAGGATGGTCGCGTCCATGCCCTGAGTCCACCCCGGGGAAGGTGACAGCATTGCTTCTGTGTAAATTATGTAC
+
#FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFF-FF-F88F-FF
@SRR6576273.3 3/2
GTTCTGGATTGTCACACAGCCCACATAGCATGCAAGTTTGCTGAGCTTAAAGAAAAGATCGATCGTCGTTCTGGTAAGAAGCTGGAAGATGGCCCCAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576273.4 4/2
GTTTTCCATCCTTGCCCTTGCAAAATAAAAATGCTGGTAGCAAGACCCCCCAACCCAATTTTACAACACTCACTAATGAAACTTGACCTGTCAACAATCC
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576273.5 5/2
GGCTCTCTGGGCCTGACTTCTTCTCTGATTGCTCTGACCACTGATTTCTGGATAGTGGCCACAGGTCCTCACTTCTCTGCCCACTCTGGCCTCTGGCCAA
+
8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576273_1.fastq

Printing command:
fastqc --outdir SRR6576273_1.fastq

Analysis complete for SRR6576273_1.fastq

Processing SRR6576273_2.fastq

Printing command:
fastqc --outdir SRR6576273_2.fastq

Analysis complete for SRR6576273_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 159M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 E5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:49 SRR6576273_1.fastq
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:49 SRR6576273_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:13 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================