-----------------------
Start of variable list:
-----------------------
Sample_ID:
P21-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 19:41:26 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790711
Current job name : Step_02_P21-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/8790711.1.linga

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 P21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6575393_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6575393_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575393_1.fastq <==
@SRR6575393.1 1/1
ANTCTTTCGAGGCCCTGTAATTGGAATGAGTCNNNTTTNAANNCTNTANNNNNNNTNNNNNGNAGGGCAAGTCTGGNGCNAGNAGCCGCGGTAATTCCAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF###FFF#FF##FF#FF#######F#####F#FFFFFFFFFFFFF#FF#FF#FFFFFFFFFFFFFFFFF
@SRR6575393.2 2/1
GCCTGAAAGGTGTGGACTTCCAGAAGTTCTGTATGAGTGGAGCAGCACTGTGTGCCCTGGGTAAAGAATGCTTCCTCGAGCTGGCTCCAGACTTTGTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575393.3 3/1
ACAGTGTTTGTTTCTAGGCAGTTACATGGCTCACCTATGCTCACTATATCCATTATAATGGTGAACAAAACACCTAGGGACAGAATAGCAAGCCCAACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575393.4 4/1
GTGCAGCCTGCCAGAAGACTGTGTACCCGATGGAGCGGCTGGTGGCAGACAAGCTCATTTTCCACAACTCTTGTTTCTGTTGCAAACACTGCCACACCAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575393.5 5/1
GAAGTGGGCTTTTGCTCATGTGTCATCTAGGGTGAAGCCTGAAAATAATGGGAATCAGTGAACAAATCCTGCTATGATAGCAAACACTGCTCCCATTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

==> SRR6575393_2.fastq <==
@SRR6575393.1 1/2
NTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575393.2 2/2
GTGATGAAGCTGGGCTCTGAGAACTCTGAGGGAGGAACACACTGAGCATGCTCGATACCGTAGCTGATGAAGTAATCCGAGGTGTAACAGGATTCTGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575393.3 3/2
ATTTATCAGAGGACTGCAGCCTATGGCCACTTTGGTAGGGACAGCTTCCCATGGGAAGTGCCCAAAAAGCTTAAATATTGAAAGTGTTAGCCTTTTTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575393.4 4/2
CCACTGCCCAGCGGGAGGCCATGTGCTGGGAGGGAATGGGTGTTAAAGGGGTCTCAGGCCGTCTTGGTGCCTGAGTCCACCTCCTTGTGGGCCCAGAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575393.5 5/2
GGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF8FFFFFFF

Starting FASTQC command


Processing SRR6575393_1.fastq

Printing command:
fastqc --outdir SRR6575393_1.fastq

Analysis complete for SRR6575393_1.fastq

Processing SRR6575393_2.fastq

Printing command:
fastqc --outdir SRR6575393_2.fastq

Analysis complete for SRR6575393_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 200M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 P21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 100M Oct 12 19:41 SRR6575393_1.fastq
-rw-r--r--   1 kkarri waxmanlab 100M Oct 12 19:41 SRR6575393_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:59 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================