-----------------------
Start of variable list:
-----------------------
Sample_ID:
G8-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 19:46:09 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791212
Current job name : Step_02_G8-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/8791212.1.linga

Loading required modules...


List files in scratch directory:

total 80M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:46 SRR6575897_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:46 SRR6575897_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575897_1.fastq <==
@SRR6575897.1 1/1
GNACATGGGCACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCNGTGACGTATGATGGATTC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575897.2 2/1
GTACATGGTAGTTCAGCCAATAGATGCCTAGTACGCTGACGGCATTCAGAGTACGCTGATCGGCTTATGACGTATGTGACGCAGCTCTTAGCGCAATGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575897.3 3/1
GTATCAACGCAGAGTACATGGGGCTCCTCAGCCTCGGTCACCACCCAGCTCTGGGACAGCAAGCTGAAAATGACTCCCTCCATCTCATGGGGTCTACTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575897.4 4/1
ATTTATTTATTATATGTAAATACACTGTAGCTGTCTTCAGACACACCAGAAGAGGGCATCAGATCTTGTTACGGATGGTTGTGAGCCACCATGTGGTTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575897.5 5/1
ACGCGGCAGTGCATATTGCAGCTGAGCCAGCTCAATTTGAAGTTTGCCTTCTCTCGTTCTCGCCCGCTTTGCAAAAATATCTAATATCAATTGCGTGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575897_2.fastq <==
@SRR6575897.1 1/2
NGCCANTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAAC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575897.2 2/2
NATATAGGCTGCACACCTTCTGAATGAGTCACACAGCTATCGACAGAGTCGTGACCATCATCGACAGTTCGCAGCCCTATAACATGATACGAGGTCATCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFF8FFFFFF-FF8FF-F-
@SRR6575897.3 3/2
NCGTGTGAGTGTCACCCTTGCTCCCTAGGGAGAGCATAGCAAAGGCTGTGGCAATGCTCACTGGGGAGAAGAAGATGTTGGAAGTGTTGGACTGATGGAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575897.4 4/2
CGGTGAATCCTCTGCACCCAAGAACAAAAAGGGAGATTTAAAAAAAAAAAAAAAAAAAGGGGGACTGGTTAGATGGCTCAGTGGGTAAGAGCACCCGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFF-FFF---FFFFF8FF-
@SRR6575897.5 5/2
GATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCATTGGCAACAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575897_1.fastq

Printing command:
fastqc --outdir SRR6575897_1.fastq

Analysis complete for SRR6575897_1.fastq

Processing SRR6575897_2.fastq

Printing command:
fastqc --outdir SRR6575897_2.fastq

Analysis complete for SRR6575897_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 447M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 224M Oct 12 19:46 SRR6575897_1.fastq
-rw-r--r--   1 kkarri waxmanlab 224M Oct 12 19:46 SRR6575897_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:52 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================