-----------------------
Start of variable list:
-----------------------
Sample_ID:
O21-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 19:49:50 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791393
Current job name : Step_02_O21-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/8791393.1.linga

Loading required modules...


List files in scratch directory:

total 39M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 O21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:49 SRR6575193_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:49 SRR6575193_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575193_1.fastq <==
@SRR6575193.1 1/1
GTCAATCCTGTCCGTGTCCGGGCCGAGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTA
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF--FFF-FFF
@SRR6575193.2 2/1
GNATCAACGCAGAGTACATGGGGCAGATCCCTTCAGGTCCCAGCCNAGCATGGACCCCCCAGGCTACCTCCTGTTCCTGCTTCTGCTCCCAGTGGCTGCA
+
F#FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF#FFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFFFFF-FFFFFFFF-
@SRR6575193.3 3/1
GTACATCACTCCCGACCAGCTGGCTGATCTGTACAAGTCCTTCGTCCAGAACTACCCAGTGGTGTCCATCGAAGATCCCTTTGACCAGGACGACTGGGGC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575193.4 4/1
AAACAGAGGTGCCCTGTGCAGGGGTAAGAGCGAAGACTTGGGGGCTCTTGGGAGTTAAAAGGATCCCTGGGACTACGGTGTGAGTTTAGGCTTGGGTTGC
+
FFFFFFFFF-FFFFFFFFFFF8FF8FFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFF---FFF-FF--F-FFFFF-FF--FFFFFFFFF-
@SRR6575193.5 5/1
CACTTGGTATTAGTACAATGCTCAATGTATTGAAGGCAACTAAGCCTTTTTATTATTTGAGACAGAGTTTCGCCGTATAGCCCTGGCTGAAAAGGGTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6575193_2.fastq <==
@SRR6575193.1 1/2
NATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCT
+
#FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFF--FFFFFFFFFFFFFFFFF-FFF--FFFF-FF
@SRR6575193.2 2/2
NGACTCTACCATCTTCTTGGGCAGGCCTGCCGTGTGGGCGCATACATACAAACACCACCCCTACAATTAGGAGTGACATGACCGCATCTGCAGCCACTAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FF-FFFFF-FF
@SRR6575193.3 3/2
GATCTGCCCAGTGCAGAGCCCCACCACCAGGTCTGCGATGAAAGTGTCCTCAGTTTCCCCAGATCGGTGGGACACCATGACGCCCCCAAAGCCATTGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF8--FFFF
@SRR6575193.4 4/2
GTTCAGTCCTGAGGATCTACACAGTACAAGGATAAAATCAAGTCCCACGGGTTATCTTTTGCCCTTCACAGGAGCTTCACAGCACTCATCCATGTGTGTA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-F8FFFFFFFFFFFF
@SRR6575193.5 5/2
GAATTGTTCTCTGAGGAGCAAGCGTCTTATTCCAGGACTTTTCTGCTGTGGTCTAATGATATACCCAGCAGGGAATATGGCAGAGTCCAACCCTTTTCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575193_1.fastq

Printing command:
fastqc --outdir SRR6575193_1.fastq

Analysis complete for SRR6575193_1.fastq

Processing SRR6575193_2.fastq

Printing command:
fastqc --outdir SRR6575193_2.fastq

Analysis complete for SRR6575193_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 191M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 O21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  96M Oct 12 19:49 SRR6575193_1.fastq
-rw-r--r--   1 kkarri waxmanlab  96M Oct 12 19:49 SRR6575193_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:05 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================