-----------------------
Start of variable list:
-----------------------
Sample_ID:
F1-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 19:44:29 EDT 2018
Running on node : scc-yb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791148
Current job name : Step_02_F1-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/8791148.1.y

Loading required modules...


List files in scratch directory:

total 66M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:44 SRR6575855_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6575855_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575855_1.fastq <==
@SRR6575855.1 1/1
GGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCATGACGGACCAGAGCGAAAGCATTTGCCA
+
FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575855.2 2/1
GACCATTGGATACGGCAGCTTCCAGCATGCCGAGGGAGTGAGGGAGGCAGGGAGCCGGCAGGCAGCGGGCTCTCACTTCTTCCACTCATTCTTGTCATAG
+
FFF8-8--FFFFFF8FFFF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF-FFF
@SRR6575855.3 3/1
TACCAAGTGCATCAGCTTCCGTGACCACATGAAGACCGTCCTTCCGCCTGATGGCCCCCGGCTTGCCTGTGTGAAGAAAACCTCCTCTCCGGATTGCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575855.4 4/1
AAGCTTTTGTTTGTTGTTCCCCTGTTGTGACTTTGAGTGGACAAGCCTACAAAATCTTGAATGCCAGGTATTTGTGAAGACAGTATAAGTTTAAAGGGTC
+
FF8FFFFFFF-F-F8FF8FF8FF8888FF8FF8FF-8FFFFF8FFFFFFFFFFF---FFF-F-FF-FFFF--FFFF-FFFFFF--F--FF-FFF-F-F-F
@SRR6575855.5 5/1
TTTTTGGCTCCTTCCGCATTTATTGGAGAAAACAGGCAGAAGGTAGGGAGAGGGGCTCTAGCGGTGGCCAGTGGAGCAGCTGGGGTGGGAAGACTGGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFF-

==> SRR6575855_2.fastq <==
@SRR6575855.1 1/2
NTCCACCAACAAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGACCGGGCCGGGTGAGGTTTCCC
+
#8FFFFFF-F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFF-FFFFFF-FFFF-FF--FFFFFFFFFFFF
@SRR6575855.2 2/2
NGACTACCCCTTGCCTGATGTGGCCCATGTCACGATGCTGTCTGCCAGCCAGAAGGCGCTGAAGGAGAAGGAGAAGGCCGACTGGAGCAGCCTTCCAGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575855.3 3/2
CAGCCACAGCGTAGTAGTAGGTCTGTGGATGTTCCACTGATCCATAAAACTCCGCCGCCACGGGCTTCAGGTTGTTCGGAGTCAGGCCGGCATCGTACAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575855.4 4/2
GTCTACCACTACACTTCCCTAGGATTTGTCTTCGTGTATTAGCTAAATCTTAGGAAGTTGGTAACAAAAACAGAAAAAAATCCAAAATGATAAGCACTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-
@SRR6575855.5 5/2
GCCATAGTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAGAGACAGGCAGACGGACCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF

Starting FASTQC command


Processing SRR6575855_1.fastq

Printing command:
fastqc --outdir SRR6575855_1.fastq

Analysis complete for SRR6575855_1.fastq

Processing SRR6575855_2.fastq

Printing command:
fastqc --outdir SRR6575855_2.fastq

Analysis complete for SRR6575855_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 352M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 176M Oct 12 19:44 SRR6575855_1.fastq
-rw-r--r--   1 kkarri waxmanlab 176M Oct 12 19:44 SRR6575855_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:49 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================