-----------------------
Start of variable list:
-----------------------
Sample_ID:
N4-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 19:42:17 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790876
Current job name : Step_02_N4-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/8790876.1.linga

Loading required modules...


List files in scratch directory:

total 23M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:42 SRR6576645_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576645_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576645_1.fastq <==
@SRR6576645.1 1/1
GAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCATTGTTATAAACGCAGAGTACATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FF-F--FF--F-F-FF-F--FFF---
@SRR6576645.2 2/1
GTATCACGCAGAGTACATGGGTCACACAGTGCTACCGAGACATCGGTGCCCGACACCGTGCCCGTGCCCACTCCATCCAGATCATGAAGGTGGAAGAGAT
+
-8-FFFFFFFFFFF8FFFFFF8FFFFFFFF8FF8F-8FFFFF8-FFFFFFFFFFFFF---FFFFF-FFFFFFFF-FF-FFFFFFFFFFF--F-F-F-FFF
@SRR6576645.3 3/1
GTGGTGGAGACGGCTGAGGAGGATGTGGGCTACGCGCGGGCTGGCGGTAGTGCTGGCCCTGAGCGTGCTGCCTGACAGCCGGGCGCTGCGGCCAGGAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576645.4 4/1
AGCTAGTATTCTCCCACTGTATGGGTCCTAAAGTTTGTCAACAGATGGTCATCCACTGAGCCATCTCCTTGCTCTCCAGTTACAAACAAACAAACAAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576645.5 5/1
CCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF

==> SRR6576645_2.fastq <==
@SRR6576645.1 1/2
GTATCAACGCAGAGTACATGGGTTAGCAATTTAATGCGGTAGTTTATCACATTAAATTGCTAACCCATGTACTCTGCGTTGATACCACTGCTTCCCATGT
+
FFFFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFF-FF-FFF-FFFFFFFF--FFFFFFFFFFFFFF
@SRR6576645.2 2/2
TCTTGGAGTCGTGGAACTGCTTGACAGCTGGCCGGCGGCACTTGCCAGCTGCAATCTCTTCCACCTTCATGATCTGGATGTAGTGGGCACGGGCACGGTG
+
-----FF--F8FFFFFFFFF8F-FFF-FF-F-FFF-F-FF--FFF--FF--FFF-FF-FF-FFFF--FFF-FFF-F-F-F-FFFF-F-FFFF-FF8--FF
@SRR6576645.3 3/2
CTTCAATAGTGGCTGGTGAAAATGTGACATCTCTGTCTTTGAGGTCCTGGTAAAATCGTCCCAGATAAGAAATACAAACTTCACAGTCTCCTGGCCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576645.4 4/2
GTCCAGACCTGTGTCTCCTAGAGATCCATTCAAGTTGACGACGAAGAGTGACCATACATACAACTGATAAATTGAGTGGCATTGCTAATAATATGACTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFF8
@SRR6576645.5 5/2
GGATGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAAT
+
FF-FFFFFFFFF8FFFFFFFFFF8FFFFFFFFF-FFF-FF-FF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-F-FFFFF88

Starting FASTQC command


Processing SRR6576645_1.fastq

Printing command:
fastqc --outdir SRR6576645_1.fastq

Analysis complete for SRR6576645_1.fastq

Processing SRR6576645_2.fastq

Printing command:
fastqc --outdir SRR6576645_2.fastq

Analysis complete for SRR6576645_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 106M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:42 SRR6576645_1.fastq
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:42 SRR6576645_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================