-----------------------
Start of variable list:
-----------------------
Sample_ID:
K18-MAA000377-3_9_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 19:41:27 EDT 2018
Running on node : scc-pe2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790833
Current job name : Step_02_K18-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790833.1.p

Loading required modules...


List files in scratch directory:

total 32M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 22 root   root       12K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576525_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576525_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576525_1.fastq <==
@SRR6576525.1 1/1
CTGTGCCTGCTGCCCACCATCAGCTTTCCTCAGCACCACACTTGCTTGCATTCTGTGCCTGCCGCGCTGCCTTACACTAGTATGCTAATGACCAAAGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576525.2 2/1
CTTTATTGGATTTGAGCCAGGGGAGGTGACACTATTTTTCCAGACTTCAAAGGAGACTGCTATAGCATAGGTCACCTGACCATCTTAAACAGCAATAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F
@SRR6576525.3 3/1
GTGGTGCAGACTGCAAAATGGGAAGCCAGGAGTCCTTCACCATAATGCCCACCTCTCCCGTGACCCATAACTCACTGGGTGCAGTGATTGGCATTGCAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576525.4 4/1
ACATAGTACTTATCCAAAAGATAAGGTGCTATGTTGGGCCAGCAACACTGCACTGCAAAGAAAATAAAAAATAAAAACCACCCAGGCAAAAATGGCATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576525.5 5/1
TTGGTGGACAGGCCGGCCAATTCCCTGGGTGAAGGGGGCCCCACCTTTGGACAATCCCCCCTGTGCCTTTGACTTGGACGACCCATCCTGTGATAAAACT
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576525_2.fastq <==
@SRR6576525.1 1/2
ACTTAATATAAATGAAGCTTTAAAAAAGGATATAAAAAGCAATTCATAGACAATATTAATAACTCAGACATTGGACTGAGAGATATGGGAAGGTCACTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576525.2 2/2
GGTCTACACTCTGGAGAGAGAGGACCCGGGTGAGGAGGACTAGGTGCCAGCCCTGCCCAGTGTCCCTGTGCCCTCTCCTGGGTTAGTCCACATGTCGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576525.3 3/2
ACATCTGGCATGACGTAATCAGAGCCATCCAGCCGCCCAGTGCTGTAAGCCACTGCCAAGTGCTCATGTTCCTTGCCCTTTTGCCACTGGCGGTAGCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576525.4 4/2
GCCTTATAGCAACAAGAAAGCCAGAAACTGAGCAACTTGGGCCACAGATGGGTAGGACCACTGTAGAACAAGAGAGGCACACACTTTCTTGCCAAATGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8FFFFFF
@SRR6576525.5 5/2
TCTGGACAATCTCCTTGGGACTGAGGTCCAGGCCTTCCAAGTAGAAAGGACCACTTCGAAGTGCTATTTCCTGTAGAATGATGGCAAAGCTGTAGACATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFF-FFFFF-FFFFFFFFFFFFFF--FFFFFFFF-FFF-FF-FFFFF--FFFFFFF-F-8FF

Starting FASTQC command


Processing SRR6576525_1.fastq

Printing command:
fastqc --outdir SRR6576525_1.fastq

Analysis complete for SRR6576525_1.fastq

Processing SRR6576525_2.fastq

Printing command:
fastqc --outdir SRR6576525_2.fastq

Analysis complete for SRR6576525_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 164M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 22 root   root       12K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  82M Oct 12 19:41 SRR6576525_1.fastq
-rw-r--r--   1 kkarri waxmanlab  82M Oct 12 19:41 SRR6576525_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================