-----------------------
Start of variable list:
-----------------------
Sample_ID:
F9-MAA100140-3_57_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 19:46:09 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791183
Current job name : Step_02_F9-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791183.1.linga

Loading required modules...


List files in scratch directory:

total 124M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:46 SRR6576086_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:46 SRR6576086_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576086_1.fastq <==
@SRR6576086.1 1/1
GTGCCCAGGCTGTGGCTGCTCCTCCACTCAACCATTCTTTGGCTACGTAGGCGCATTCAAGTGTCTGAAAGATGGCGGTGGGGATGTGGCCTTTGTCAAG
+
FFF8FFFFFF-FFFFFFFFFFFFFFFFFFF8FFF8FFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFF-
@SRR6576086.2 2/1
ATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTGGACTTGCCTTTGAAGCCTGCTTTCCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576086.3 3/1
CTTCTCATGCAGCAGACACACACGGTTCAGGATTGCAGACAGATAGTCTTCCACACAAGGCAGTCTCTGATCTTCAGGAAGTGTACAACACTTGGTGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576086.4 4/1
GTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576086.5 5/1
CTCCTACACCTACCTCTCTCTGGGCTTCTTTTTTGATCGGGATGACGTGGCTCTGGAGGGCGTAGGCCACTTCTTCCGCGAATTGGCCGAGGAGAAGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576086_2.fastq <==
@SRR6576086.1 1/2
NCCCAGTGTGGCAGGACTTCATGCCTATCAGGTAGTTCCAGGTGATGCTAGTGTCCGATGCCTTCACCACAGCCACGGCATAATACCATTTAGGAAAGAT
+
#-FFFFFFFFFFFFFF8-FF88FFF--FFF--F-FF-FFFFF--FF--F-FFFFF-FF---FFF-F--FFF-FFF--F-FFFFFFF----F-FFFF8F8F
@SRR6576086.2 2/2
NTGTAGACATACATGATTCTATTCAACCAAGATCTTCAGATAACAGACAGCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGT
+
#FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFF8FFF8
@SRR6576086.3 3/2
CGTCTGAGCCAGACATTCCCCAATGCTGACTTTGCAGAAATCACCAAATTGGCAACAGACCTGACCAAAGTCAAAAAGGAGTGCTGCCATGGTGACCTGC
+
FF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF-F-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576086.4 4/2
ACCATACTCCCCCCGGAACCCAAAGACTTAGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGG
+
FFFFFFF-FFFFFFFFFFFFFFF8FFFF--FFFFFFFFFFFFFFFFF-FFFF--F--F-F---FFFFF-FFFFFFF-FFFFF-F-F-F---8-FF-FFFF
@SRR6576086.5 5/2
GAACCCAGGGCATGCAGATCCAAGAGGGCCTGATTCAGGTTCTTCTCCATGGCCAAGGCAGCTTCCATGGCCTCCTGGGTTTTACCCCATTCATCTTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576086_1.fastq

Printing command:
fastqc --outdir SRR6576086_1.fastq

Analysis complete for SRR6576086_1.fastq

Processing SRR6576086_2.fastq

Printing command:
fastqc --outdir SRR6576086_2.fastq

Analysis complete for SRR6576086_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 666M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 333M Oct 12 19:46 SRR6576086_1.fastq
-rw-r--r--   1 kkarri waxmanlab 333M Oct 12 19:46 SRR6576086_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:45 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================