-----------------------
Start of variable list:
-----------------------
Sample_ID:
K14-MAA000377-3_9_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-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790831
Current job name : Step_02_K14-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790831.1.linga

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root      132K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576492_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576492_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576492_1.fastq <==
@SRR6576492.1 1/1
ACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGTTGAATGGGGAGGAGCTGACCCAGGACATGGAGCTTGTGGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576492.2 2/1
ATTCTACATTCTCTATCCTCAGCCAAAGGCCAGTTCTAAAACCTGAAGGAAGGGCATTTTGCTCAAGCTGATGCTGCTTTAAAATTGTGACCTACAAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576492.3 3/1
GTCATTCCCTGTCCTCCTAACACAGTGCCAGCAGTGGGACAAACTTTAGCTTTAATACCAGCCACCCCATAAGTACAAATAGTAGAAAAGGAGCTAGCGA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576492.4 4/1
GGGTGTTGTGGGGCAGGCCCCCCAAGCTGATGATCATGGGAGCAGGGCTCTGACAGCCCTTATCCTCTCAGACTTGACAGATGGGGCAGAGGAGGGACCT
+
FFFFF8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576492.5 5/1
GATCCCGCCCCCACTATTCTCCTGCTCTAATTGTTCATTGTTTTACTTTTTTCTCAACTCTAACTTTTTTCTCAAAATTGTTAATAATTATCAGTGTCTT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFF8F8F8F8FF8FFFFF8--FFF--FFFF---F-FFFFFFFFFF-F-F---FFF-F-FF--F-F-F-FFFFF-F

==> SRR6576492_2.fastq <==
@SRR6576492.1 1/2
ACCCAATCATGTCCACATTGCCCCTCCCCAATCAGACCCTAGAGTGTCACCTTTACAATCTCGGAGAGACATTTCAGAGCTCTGGGAGCCTGGAGCCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF-FFFFFFFFFFFFFFFF8FFFFFF8-FF-
@SRR6576492.2 2/2
GCCTTGCATGTGGCCTTTTGCAATGGGCTCTGACTTTCCTTTCAGTACAGAATGAATGGGTAGTGGTGGTTTCTGGATTCTGAGTAGATGGAGCTGTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576492.3 3/2
GTGTAGGGTCAATCTCTTCGAAAAAATTAACACCCCCACCATTAGGAAGAATTTGTAATTCTTTTCTTTTTAGGCAAATGTAATAATCAACTTGGAGATT
+
FFFFFFFFFFFFFFFF8FF8FFFFF8FFFFFFFFFFF---FFFFFFFFFFFFFF----FF--FFFFFFFFFFFFFF-FFF-F---F-8--F--FF-FFFF
@SRR6576492.4 4/2
GGCTGGCCACCCCCATCAATGTCCCCACTTGCTCCCAGCCTAGCTGTGCTGAGGACTAGGGAAGAGCTGTAGGGCCACCCGAGGCAGAGCCCAGGGAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576492.5 5/2
CACTGTGGCTCTGCAGACCTGCTGATGCTACTACAGAACTTTCCTGGGCCTTTCTCTCTTATGCTCAGAGAAGGTCAATGAGTTGTTGATGATACACATC
+
FFFFF8FFFFFFFF8FFF8FFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8-8--F

Starting FASTQC command


Processing SRR6576492_1.fastq

Printing command:
fastqc --outdir SRR6576492_1.fastq

Analysis complete for SRR6576492_1.fastq

Processing SRR6576492_2.fastq

Printing command:
fastqc --outdir SRR6576492_2.fastq

Analysis complete for SRR6576492_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 174M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root      132K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  87M Oct 12 19:41 SRR6576492_1.fastq
-rw-r--r--   1 kkarri waxmanlab  87M Oct 12 19:41 SRR6576492_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:43 EDT 2018
0 hours, 0 minutes and 16 seconds elapsed.
==========================================================