-----------------------
Start of variable list:
-----------------------
Sample_ID:
L7-MAA000907-3_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 19:41:28 EDT 2018
Running on node : scc-yb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790852
Current job name : Step_02_L7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790852.1.y

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576559_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576559_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576559_1.fastq <==
@SRR6576559.1 1/1
TCTGGGGCTGGAGAGTTGGTTCAACAGTTAAGAACCCGTGTTGCTCTCTCCCAGACGACCCAGCGACTTGTGAGGCTCATAACCAGCAACTCCAGCCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.2 2/1
TCCCAGTTGAGAAAGCAAGTACTTGAATATCTCCATAGGTATTCATGACAATGGTTTTGGATTTCTGATCCAGTAGCCTAAGACAAAAATTTGTGTTGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.3 3/1
CTGTAGAATGGGGCCGGCGCCGCGCATCCTGGAACTCTTCTACGACGTGCTGTCCCCGTACTCCTGGCTGGGCTTTGAGGTCCTATGCAGATACCAACAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.4 4/1
CGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.5 5/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTAAGCGATTGCATTTTAAAAAGTTAGGGAGATTTGCCTTATATTTTATAAAAAAAAATAATCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8--8-F----FFF-FF-F-FFF-F-F------F--F----F-F--FFF--F--F-F-----

==> SRR6576559_2.fastq <==
@SRR6576559.1 1/2
NGACATCACTCATCGATGTCATCTCTACCAGAAGGGAGAAGATTCTGGAGTGCACATCGGTTACCGGGCTTCGCGTGTGGAAGTGGCCCACTGGGTCCAG
+
#F-FFFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF--FF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.2 2/2
GGCTTAGGCCTTTAAATCCTCCAGTTCACAATCTGAGCATCACTTTAGCTCTCTGAGACACTCAGCTAGCTCCCCTCCTACCTGAGCTCCCTTTCTATGC
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.3 3/2
GGGTATGTTGAGGGGAACCTGGAAGAACTGCTTCAGGAGAGGAATCTCTTTGAAGATGTACTGGCCTTTTCGGGGAACCATAGCAGGTGGTTGGTTTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576559.4 4/2
GTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGTACAGTGAAACT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576559.5 5/2
GGGATTGGGGGGGTGGAGGCGGCTCCTGAGACCGAAAAGGACTTGCGACTCGCCGGCCACGCACCATGAGGGTCCTGTGGGTGTTGGGCCTCTGCTGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576559_1.fastq

Printing command:
fastqc --outdir SRR6576559_1.fastq

Analysis complete for SRR6576559_1.fastq

Processing SRR6576559_2.fastq

Printing command:
fastqc --outdir SRR6576559_2.fastq

Analysis complete for SRR6576559_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 167M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6576559_1.fastq
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6576559_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================