-----------------------
Start of variable list:
-----------------------
Sample_ID:
F9-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 19:46:08 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791182
Current job name : Step_02_F9-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/8791182.1.linga

Loading required modules...


List files in scratch directory:

total 127M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:46 SRR6575873_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:46 SRR6575873_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575873_1.fastq <==
@SRR6575873.1 1/1
ATAGATCACAGGGGGTTTTCCCAATCTCTCTCGGTGCAGTGGGATAGGACAAGAAAAGTAAAGGATGAAAACAATGTTGTAGCTCAGCCACAGTAAGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-F
@SRR6575873.2 2/1
GGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGG
+
FFFFFFFFFFFFF-FF-FF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575873.3 3/1
GGTTTCAACGCAGAGTACATGGGGAGCTGCACTGGAGCTGCCACGGTTCTTGGTCCCTACGCCTGAGCTCGTGTGCTCCAACGGGCTGCAGAATGGAAAA
+
FFFFFFFFFFF-FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F-
@SRR6575873.4 4/1
CTTTTAAGGGGGAGTACTTCCACAGCCGACAGTATAAACATCCAGACATATTTAAGGACAAGCGAGTCCTTGTAGTTGGAATGGGGAATTCTGGTACAGA
+
8FFFFFF-F-FFFFFFFFFF8FFF8F8FFFF8FFFF888FFFFFFF-FFFFFFFFFFFFF-FFFF-FFF-F-FF-FFFFFFF-FFFFFFFFFF-FFFFFF
@SRR6575873.5 5/1
TAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGAATATT
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFF-

==> SRR6575873_2.fastq <==
@SRR6575873.1 1/2
NAATACATGATAAAATCAACTCACACTTCTCTAGCATCTCTGAGTTTAAAATGCCTTCCTTTCTGTGCTGTTCTAGGCATGAGGGCAATTGTGAGGGTTG
+
#FF-FFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFF-FFFF-FFFFFFFFFF-FF--FF-FFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFF
@SRR6575873.2 2/2
NACGAAGCAAGGACTACGGGAAGGAACATTAATGTAGAAAAGAGGAAGGGGGAATGGCATACTAGTCTCCTGGCCGCTGACCCCAGAGAAAAGCTAGACG
+
#FFF--FF-FF-8FFFFFFF88-FF--F-FFFFF-FFFF--FFF----FFFF-FF-FF-FFFFF-F--FFF-FFF-FFFFFF--FFF-F--FF----F-8
@SRR6575873.3 3/2
NCCCAAGGAGACGTGAAAATAGACTGGGAAGACCTTGCTCTGCACCAGTCCAAATGTGTGCCGCGGGAGGCTCCGAAAAAGCAGGAAGCCTGAGATAAAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FF-FFFFFFF8FF8F
@SRR6575873.4 4/2
CTTGTACAGTGATGCCTGGCCATCCTCAACATTCACTACGGATTCATCGAGCAAGGTGAACGCAAAAGTATATCCAGTCGCAAAGACAAAGATGTCAAAG
+
F--F-FFF-FFFFFFFFFFFFFF8FFFFFFFFF-F-FF--FFFF-F--FFF-FF---F-FFF-F-FFFFF-FFFF-F-FFF-FFFFF-F---F-FF8F-F
@SRR6575873.5 5/2
CACTAAATCATGGCCTCAGATCCGAAAACCAACAAAAAAGAACCGCGGTCCTATACCATTATTCCTAGCTGCGGTAACCAGGCGGCTCGCGCCTGCTTAG
+
F-FF-FF-FFFFFFFFFFF8FFFFFFFFFFFFFFF-F-----FF-FFFFFFF---FFF---FFF-FFFFFF-F--F-FF8--F--F-F---FFF-F---8

Starting FASTQC command


Processing SRR6575873_1.fastq

Printing command:
fastqc --outdir SRR6575873_1.fastq

Analysis complete for SRR6575873_1.fastq

Processing SRR6575873_2.fastq

Printing command:
fastqc --outdir SRR6575873_2.fastq

Analysis complete for SRR6575873_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 646M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 25 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 323M Oct 12 19:46 SRR6575873_1.fastq
-rw-r--r--   1 kkarri waxmanlab 323M Oct 12 19:46 SRR6575873_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:44 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================