-----------------------
Start of variable list:
-----------------------
Sample_ID:
C6-MAA100040-3_11_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 19:44:28 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791033
Current job name : Step_02_C6-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791033.1.linga

Loading required modules...


List files in scratch directory:

total 59M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575156_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:44 SRR6575156_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575156_1.fastq <==
@SRR6575156.1 1/1
TNCACACTGTGGCAGATGGACACGGTTCCTCTAACATGATAGAGATTATGTGGGTTTCCTAGTTCCTGTGTGTCTTAGTTTNGTGATGGTTCCCTTTGTA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFF--F-FFFF
@SRR6575156.2 2/1
GTACATGGGACTTTAAGGGCTCAGAGATGGTGGTGGCTGGGAAGCTCCAGGACCAGGGTCCTGATGTCCTCTTAGCCAAAGTCAGTGGGCAGATGCACAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575156.3 3/1
CCCGGGGAAGAACATCTACTATAAGAGTGACCTGACCAAGGACATTACGACGTCAGTACTGACAGTCAACAACAAAGCCCACATGGTAACCCTGGACTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575156.4 4/1
GTGCAGCCCTACCTGGACGAATTCCAGAAGAAATGGAAAGAGGATGTGGAGCTCTACCGCCAGAAGGTGGCGCCTCTGGGCGCCGAGCTGCAGGAGAGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575156.5 5/1
GGCCTGCAATGTAGGCATGTCCTCCATCCAAAGTCATGGCGTCCGCTTCTCCGTTCACAATCTTTTCAATGCAGTCCTCAGTGGTCTCTGCTGACTCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575156_2.fastq <==
@SRR6575156.1 1/2
NTAAANGCCATTTCATATATATAATATACAGAAATTATTTTAAAAGTCTGTCATATAACAGATTCATTTGGTGCTACCAAAAACTTACGATACAAATAAA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575156.2 2/2
NTGAGAGGGGTGACAAAATTGTACTTGAGTGACAAGTTCAGAACTTGGGCCTCGAGGGCCTCTAATTCGGCACCTGACGCTGAAATCCTCTGCTCCAGCT
+
#8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575156.3 3/2
NTATTGTTTACTCCGTTTGCCCGACCCCCACATCTGCACCCAAATGCAATATCTGCATTAGGGGATGGTCTTAGGGTAGGGGCCATTGCCTGAGCATGGG
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--FFFFFFFFFFF-F-FFF-FFFFFFF8FFFFFFFFFFFFFFF
@SRR6575156.4 4/2
AGGTCTGGCTTTCTCGCCAAGTGTCTTCAGGTGGGTTTTGGCCCTGGTGTGGTACTCGTTCAAGGTAGGGTTGCTCTTGAGCTCAGCCAGGCGCTGGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575156.5 5/2
AGTATGAGGATTGCTACCTGGCTCAGATCCCTTCTCATGCTGTTGTGGCTCGAAAAAACAATGGCAAGGAAGACTTGATCTGTGAGATTCTCAAAGTTGC
+
8FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF---FF-FFF-FFFFF8--F-

Starting FASTQC command


Processing SRR6575156_1.fastq

Printing command:
fastqc --outdir SRR6575156_1.fastq

Analysis complete for SRR6575156_1.fastq

Processing SRR6575156_2.fastq

Printing command:
fastqc --outdir SRR6575156_2.fastq

Analysis complete for SRR6575156_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 339M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 170M Oct 12 19:44 SRR6575156_1.fastq
-rw-r--r--   1 kkarri waxmanlab 170M Oct 12 19:44 SRR6575156_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:51 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================