-----------------------
Start of variable list:
-----------------------
Sample_ID:
H1-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-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791231
Current job name : Step_02_H1-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/8791231.1.linga

Loading required modules...


List files in scratch directory:

total 119M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:46 SRR6575908_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:46 SRR6575908_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575908_1.fastq <==
@SRR6575908.1 1/1
AGTCTGCAGTTTGCTGGAGATAGTCGCCTGGTTTTCACACATGTACTTGGCAAGTTCCGCCCTGTCATCTGCGCATTCCAGCAGGTCACCATGGCAGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575908.2 2/1
CAGTAGTCCTACTCATGTTTCAAGTTTCATGTCCCAACCAGCACCTTGGCCACATTCCTGGATCCTATGCTTGTCCCAGAGGAGAAGGCTGCAGAGATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575908.3 3/1
CTGATCCACTGGCTTGCGGGTATTGTCAAGGCAGAGCAGTTCATATTGGTCCCTGTCAGCCTTCTCCGGCAAGACCTCAAATATGGTTGTGTGCTTGACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575908.4 4/1
GAGATGAGCTCCTTGTTGAGAGTTTGCTCCAGATGCTGCATCTTCCCATCTTCGGGCAGGAGGAAGACAGCACTGGCGTAGCCCGCGTAATCCATCAGCA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFF-FFF-FFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFFFF
@SRR6575908.5 5/1
GTTCCAGGTACAGGATGGCAAAGCTCTGATAGTCAGTCTCAGCAACCACCATATGCACTGGTCCACGGGCCCGTGAGACTTGGAACAAGAAGCGGCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575908_2.fastq <==
@SRR6575908.1 1/2
NAGCCCGAAAGAAACGAATGTTTCCTGCAACACAAAGATGACAACCCCAGCCTGCCACCATTTGAAAGGCCAGAGGCTGAGGCCATGTGCACCTCCATTA
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFF-FFFFFFFF-FFF-F-FFFFFFFF-8-F
@SRR6575908.2 2/2
NTGCAGCAGTTCTCACTGAAGGCAGCACCTGGACCATGGCAGGGGTAATTCTGTTCAGCCTGGGCTCAGTCCACCTACAGACCTTGCTGTGATGGAGTCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFFFFFFFFFFFFFFFF
@SRR6575908.3 3/2
NGCCTGGGAAGGTCTGCAGGCTGGGTCATCCCCATTGGCTTGCTCTTCTGTAAGCTGTCGGAGCCCCGCAGTCCTCTTGAGAAAGCTGTGTCCAGTTTCT
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575908.4 4/2
NGCCCCAGCCTCCCATGAGATCGCTACAATCCTGGGAGACTTTGCCATCAGCCTATACCGGGAGCTGGTCCATCAGTCCAACACTTCCAACATCTACTTC
+
#-F-FFF-FF8FFFFFFFFF8FFFFF-FF-FF--FFFF--FFF-FF--FFF-FFFFFFF--FFFFF-FFFFFFFF---F-FFF--FFFFFF-FF8-F-FF
@SRR6575908.5 5/2
NGGCTGTGTTGTTCTTCACCCTGCTCTTGACAGCCAGTTCGCTGGGCCAAAGGACTCGAAAGCCTATTGGGTCTACCTCCCCCATCAGCACTATCCAGGC
+
#FF-FFFFFFFFFFFFFFFFFFFF-FFFFFF-FFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575908_1.fastq

Printing command:
fastqc --outdir SRR6575908_1.fastq

Analysis complete for SRR6575908_1.fastq

Processing SRR6575908_2.fastq

Printing command:
fastqc --outdir SRR6575908_2.fastq

Analysis complete for SRR6575908_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 657M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 329M Oct 12 19:46 SRR6575908_1.fastq
-rw-r--r--   1 kkarri waxmanlab 329M Oct 12 19:46 SRR6575908_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:42 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================