-----------------------
Start of variable list:
-----------------------
Sample_ID:
G6-MAA100138-3_56_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 19:46:09 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791206
Current job name : Step_02_G6-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791206.1.linga

Loading required modules...


List files in scratch directory:

total 65M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6575893_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:46 SRR6575893_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575893_1.fastq <==
@SRR6575893.1 1/1
ACCCAGTTCAGCCCTGCCCGAGTCCCCCAGTCATGAACCTCTTCCGATTCCTGGGAGACCTCTCCCACCTCCTAGCTATCATCTGTCTCTTATACACATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFF-FF-FFFFF-FFFFFFFFFF-FFFF-FFFFF
@SRR6575893.2 2/1
GCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575893.3 3/1
CTGCTTCCCATGTACTCTGCGTTGATACCACTGCTTCCCATGTACTCTGCGTTGATACCACTGCATCCCATGTACTCTGCGTTGATACCACTGCTTCCCA
+
FFFF--FFFF-FFFFFF8FFFF8F88FFFFFFFFFFFFFFFFFFFFF-FFFFFF-F--FFFFF--FFFF--FFFFF-F-F-F--FFFF-FFFF--FF---
@SRR6575893.4 4/1
ACCCATTCCCACAGCCCAGCTGGTACAGAGAGTAGCCTCTGTGATGCAGGAGTACACGCAGTCAGGTGGTGTTCGTCCATTTGGTGTTTCTTTACTCATT
+
8FFFFFFF-FFFFFFF-FF8FFFFFFFFFFFFFF8-FFFFFFF-FF-FFFFFFFFFFFFFFFFFF-F--FFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-
@SRR6575893.5 5/1
ATCTTGGTCATGTCTTCCATTTGATAGTTAGGATTTCTGTTTCTGCCTTGTTGAAATTTGTCTCCAGGGCCATTGTAATTCCAGCTATTCGTACTACGTA
+
F8FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFF

==> SRR6575893_2.fastq <==
@SRR6575893.1 1/2
NTGATAGCTAGGAGGTGGGAGAGGTCTCCCAGGAATCGGAAGAGGTTCATGACTGGGGGACTCGGGCAGGGCTGAACTGGGTCTGTCTCTTATACACATC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575893.2 2/2
NGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTG
+
#-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575893.3 3/2
GTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGA
+
-FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF8F
@SRR6575893.4 4/2
AGAAATAAGTCTGCACAAACAAAACATACTTTAAACATGAAAAAGTCGAGTGTGTGAGCACATCTTCATCACGCTATGGCAGCCAGGTAATCCCTCACTT
+
F8FFFFFFFFFFFFFFFF-FFF-F-FFFFFFFFFFFFF-FFFFFFFFFFFFFF-FF-FFFFFFFFFF-FFFFFFFFF-FFFFFFFF-FFFFFF-FFFFFF
@SRR6575893.5 5/2
GACAGAGAGAGCTATAGTCAGCCACCAAGACACCATCGTGGACCCCCACAGAGAGACTGGAAATGGGAAAAGGATGGCTTTAATAGTACTAGAAAAAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFF

Starting FASTQC command


Processing SRR6575893_1.fastq

Printing command:
fastqc --outdir SRR6575893_1.fastq

Analysis complete for SRR6575893_1.fastq

Processing SRR6575893_2.fastq

Printing command:
fastqc --outdir SRR6575893_2.fastq

Analysis complete for SRR6575893_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 360M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 180M Oct 12 19:46 SRR6575893_1.fastq
-rw-r--r--   1 kkarri waxmanlab 180M Oct 12 19:46 SRR6575893_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:31 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================