-----------------------
Start of variable list:
-----------------------
Sample_ID:
P6-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 19:41:26 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790712
Current job name : Step_02_P6-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/8790712.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 38 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 P6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.8M Oct 12 19:41 SRR6576748_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576748_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576748_1.fastq <==
@SRR6576748.1 1/1
TTTGAAATACAGCTCACTTGAGTTCAACTGGCACTAGAGGTTGTGCCTGCAGAGGATGGACAGAAGACAGACCATCCAAACAGAAAAGGATTGTGCAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.2 2/1
GCTGACTACTATGGTTTCTTTACCTCTTTTTACCAATATTTCCCTACTGCTGTTTAGTAAGATTTCTTTAACTCTGTTTACCAAAAGTTCCCTATCGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.3 3/1
GCCACACCAAGAGGGTTGGCATCGTGGCCTGGCACCCCACAGCCCAGAATGTGCTTCTCAGCGCAGGTTGTGACAATGTGATCCTGGTGTGGGACGTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.4 4/1
GCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.5 5/1
TGGTAGTAGTGTATGCCTTTAATTCCAGCACTTGGGAGTCAAGACACAGGTGCATCTCTTTGAGTTCAAGGCCAGTCTACAGAGTGAGTTCCAATTAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF

==> SRR6576748_2.fastq <==
@SRR6576748.1 1/2
NATGTGAGTAGAGTAGAGTATATGTGAGTAGAGTATATGTGAGTAGAGTATATGTGAGTAGAGTATACGTGAGACTTGAGAGGCTGCTTTAAAGCCCAGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.2 2/2
CTACCATTGTTTACCAAAATTTTCTTAACTCTGTTTCCAAAGTTTTCTTCCTACTGTTTACCAAATTTTTCCTACCACTGTTTACCAAAATATCCCTACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576748.3 3/2
CAATGTTGGTATCAGGATCAAAAAAAGGTAGCAGGACTCCGCTGCTTGTGTCCAGCTCCTGCAGGGACAGTGGCTCCTCCAGGTGCTTTGTGTCCCACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576748.4 4/2
CCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF
@SRR6576748.5 5/2
GGTATCAACGCAGAGTACATGGGGAGTGGCCTTGGTCTCGATACTTCGGTGTGGTTGTGAAATCTGTCCGGCAGCCTCGGGCCTGCGGTCTTGAGACGGA
+
FFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFF-F-FFFFF--FFFF-FFFFFFFFFFF--F-FF-FFFFF-FFFFFF-FFFFFFFFFFF-FFF8FFFF

Starting FASTQC command


Processing SRR6576748_1.fastq

Printing command:
fastqc --outdir SRR6576748_1.fastq

Analysis complete for SRR6576748_1.fastq

Processing SRR6576748_2.fastq

Printing command:
fastqc --outdir SRR6576748_2.fastq

Analysis complete for SRR6576748_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 111M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 P6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:41 SRR6576748_1.fastq
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:41 SRR6576748_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================