-----------------------
Start of variable list:
-----------------------
Sample_ID:
H1-MAA100042-3_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 19:46:09 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791230
Current job name : Step_02_H1-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791230.1.linga

Loading required modules...


List files in scratch directory:

total 187M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 101 root   root      180K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  91M Oct 12 19:46 SRR6575695_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  96M Oct 12 19:46 SRR6575695_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575695_1.fastq <==
@SRR6575695.1 1/1
GGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575695.2 2/1
CCTCCCATGAGATCGCTACAAACCTGGGAGACTTTGCCATCAGCCTATACCGGGAGCTGGTCCATCAGTCCAACACTTCCAACATCTTCTTCTCCCCAGT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575695.3 3/1
GTACATGGGACACACGATTGGGTGCTGAGGCCGCTTACGCGTCGCGCTTCCTCGTCTGCTCCGCATGTCCAGGGTGGCTTGCTCTCTTTTCCCCTCGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-
@SRR6575695.4 4/1
GTGTGTGTGTGTGTGTGTATGCTGTGAGATTGGTAAGCAATACATTAGTAAACACATCTTCATTACTCTTTTCCAATACTGGACCAATGATGTCCTAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575695.5 5/1
CCCCAGAAATGTCCCTGCTGAGGTGCAGGCCACGGGACCTGCCATCAGTCTCCCTTTCTGTGCTGTTCTTGGTCAGCTTTGTAGCATCCATGTCTACAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575695_2.fastq <==
@SRR6575695.1 1/2
NAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575695.2 2/2
NCTCACTGTCTGGTCTGTTGAGGGTTTGGAGGAGGTGTTGGAAGGACTTGTGGATGTCAGCCTCCGATGTTTGTGTGAGGTTGAACTGCAGGCCCTCTAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8FFFFFFFFFFFFFF8FFFFF
@SRR6575695.3 3/2
NCCAAGGCCCATTCCAGGTACCCCGATGGTCCACACTGACTGTGAACAGGGGTGGAATGATAGAAACGTCCTCATTATTTCTCTGAGCCTTCCTTAGGAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575695.4 4/2
NTTAGGACATCATTGGTCCAGTATTGGAAAAGAGTAATGAAGATGTGTTTACTAATGTATTGCTTACCAATCTCACAGCATACACACACACACACACACC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575695.5 5/2
CCAACACCCTGGCCCTTACCAGGCTCCAGCGGCTGCTCTCAGGGCCAGGCGTGGGGCTCAGGCTTTCTGTAGACATGGATGCTACAAAGCTGACCAAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575695_1.fastq

Printing command:
fastqc --outdir SRR6575695_1.fastq

Analysis complete for SRR6575695_1.fastq

Processing SRR6575695_2.fastq

Printing command:
fastqc --outdir SRR6575695_2.fastq

Analysis complete for SRR6575695_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 90 root   root      180K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 640M Oct 12 19:46 SRR6575695_1.fastq
-rw-r--r--   1 kkarri waxmanlab 640M Oct 12 19:46 SRR6575695_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:40 EDT 2018
0 hours, 1 minutes and 31 seconds elapsed.
==========================================================