-----------------------
Start of variable list:
-----------------------
Sample_ID:
A9-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 19:41:27 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790719
Current job name : Step_02_A9-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/8790719.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 81 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 A9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:41 SRR6575615_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:41 SRR6575615_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575615_1.fastq <==
@SRR6575615.1 1/1
TNTCATCTTTCCACAGAAGCATAGAGTTAAAGAAGGACTCTAATATCCAGATGGAGAGGCTGGTAATAAACGCGAATCNTCNCGTTCTTAGGAAGGAAAA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6575615.2 2/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAACAAACAAAAAAATAACAAAAAACCAATCAAAAGGTAAAAACAATTTTTTTT
+
-8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF----F--FFF-FFFFF-----FF-FFF------------F-FFFFFFFFF-F---FF
@SRR6575615.3 3/1
TCCTAAGTTTTTCTTGTTGAAATCTCGCTCTCCTGCGCAACGGCCTTCGCCCACCTGCCTCCCTCGACAAGGTCCCGGCGCCCTGGAGAACGCAAGATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575615.4 4/1
GAGTACATGGGGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCAGGAGTTCAAATCCCAGCAACCACATGGTGGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575615.5 5/1
GGCATGGCCATCGTTGGTGGCATGGCCCTGGGCGTGGCAGGCCTGGCTGGACTCATTGGACTGGCTGTCTCCAAGTCCAAATCCTGAAGGCAGCCTCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575615_2.fastq <==
@SRR6575615.1 1/2
NTCTANATGCATGNATGAACTCATCAGAACATCAAAACCCAAGGAAACCCTAAGAGAGAAGAATTCTAATAAAAAGAATTTTACATTGAAAACTTACAAG
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575615.2 2/2
NTACATGGGGCCTCCTTTACTTTCTGCTGGTTGCCTGCTGCCTGCTGTCGAGATGGGCAAGTTCATGAACCCCGGGAAAGTGGTGCTGGTCCTGGCCGGA
+
#FFFFFFFFFFFFF8F8F-F8FFFFF-FFF-F-FF--FFFFFFF-FF--FFFFFFFFFFFFFFFFFFFF--FFF-FFFFFFFFF-F-FFFFFFF8FFFFF
@SRR6575615.3 3/2
NCAATTAATACCCGGCGCCCGCCCGCCGCGCCGGGATTCGCCCGACTGTTGTCTTGGAAGGAGGCTCTAGGTCAGCTCTGAGGCCGCAGATCGCTTTACT
+
#FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFF8FFFFFFFF
@SRR6575615.4 4/2
NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTAGAGACCGGGGTTATTTGTTAAAGTTTTGGTTGAAAGGAAAAAAAGTTTTTAAACCGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFF-F-F-F-FF-F-------F-F-FF-----FF-----FF-F----------FF-----F--F--F-F--8--F8
@SRR6575615.5 5/2
CTGTAGAGGTAGACTACAGGGGTGCAGGAGAAAAGGGAAGGCGATGGTGAGGATGGACAGGCCCCTCTTCCAGTGTCCCCCAGGCTCCTAGGCGTCCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6575615_1.fastq

Printing command:
fastqc --outdir SRR6575615_1.fastq

Analysis complete for SRR6575615_1.fastq

Processing SRR6575615_2.fastq

Printing command:
fastqc --outdir SRR6575615_2.fastq

Analysis complete for SRR6575615_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 493M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 246M Oct 12 19:41 SRR6575615_1.fastq
-rw-r--r--   1 kkarri waxmanlab 246M Oct 12 19:41 SRR6575615_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:13 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================