-----------------------
Start of variable list:
-----------------------
Sample_ID:
C5-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 19:49:50 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791363
Current job name : Step_02_C5-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/8791363.1.linga

Loading required modules...


List files in scratch directory:

total 40M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 C5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:49 SRR6576184_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  21M Oct 12 19:49 SRR6576184_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576184_1.fastq <==
@SRR6576184.1 1/1
GNACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGTTTATACCAAAGCCCATGTACTATGCGTTTATACCACAGCATCCCNTTTACTCTGCGTTTATAC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFF88FF8-F--FF-FF--FF-F---F--F--F---F-F---F-FF#-----F--F--FF-F-F-
@SRR6576184.2 2/1
CTCCGTACGAGGATGACAGCTGAAGCTTGGTGGGAGAGTGGAGCTGGTGAGGCTGGAGGGGAGGAGGCTCCAGGCCCTGCGTTCAGTCAGAGTCACTGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576184.3 3/1
CACCAGCAGGAGCCTGGAGTTAGAGGGTGGGATGAGTCTGCCAAGCACAAATGTCCTCTGAGTGGAACCAAAGAAAAGAAGATCCGGGCCGCCCTGGACT
+
FFFFF-FF-FF-FFFFFFFFFFFF88FFFFF8FFFF8F8FFFFFFFFFFF-F-FFFFFF-F-F-FFFFFF-F-FFF-FFF----FFFF-FFFFFF-F--F
@SRR6576184.4 4/1
GGACAACTGTGTGATAATTGGGCAGCTGTCACATCTCTTAGGAGTATAGCCTAGTTTCAGAGTACAGGTAAGTGAGAAGAGGAGGTTCTCTGAGAACCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576184.5 5/1
CCCCAGAGCTGGGCTGCAGGCTCAGTCTCTGGACTCCTCTGTCTGGCAATTGTGAGGAGCCAAAGTTTTCAAAGGAGCTGATTCTCTGCCTGATGGAGGA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576184_2.fastq <==
@SRR6576184.1 1/2
NTACANGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGAAGCAGTGGTATCAACGCAGAGTACATGGGA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576184.2 2/2
NAAGAAGTCGCACAAGCATCACAAGCACGGGAAGCACTCCTCCTCTTCCTCCTCCTCTTCCAGCAGTGACTCTGACTGAACGCAGGGCCTGGAGCCTCCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576184.3 3/2
ACTCAGGGCTGAGGGCAGCCAGCACGAACATCAGTAAAAACATGCAGGAAAAAACATCACACGCCCCTGGACAGAGGGGAAAGATCCAGAACGGAAGAGG
+
8F-F-F-FFFFFFF8F8FFFFFFFF-FFFF-FFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFF-F--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576184.4 4/2
GTGAATGATAACTTATCAGAAAGGGGAAAAGGATCCTGGTGCTTTCTCTGTACAGCTTGTGAGGCAGACTGATTCCTCTCAACTGGGCAGACAAAAATCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576184.5 5/2
CATCATGAGTGAGAACCATAGCCATACACCACTACAGCCCAACACCAGCCTTGGTGAAGAGGATGGGACACAGGGCTGTCCAGAGGGGGGCCTGTCAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---FFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFF8FFF

Starting FASTQC command


Processing SRR6576184_1.fastq

Printing command:
fastqc --outdir SRR6576184_1.fastq

Analysis complete for SRR6576184_1.fastq

Processing SRR6576184_2.fastq

Printing command:
fastqc --outdir SRR6576184_2.fastq

Analysis complete for SRR6576184_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 213M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 C5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 107M Oct 12 19:49 SRR6576184_1.fastq
-rw-r--r--    1 kkarri waxmanlab 107M Oct 12 19:49 SRR6576184_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:16 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================