-----------------------
Start of variable list:
-----------------------
Sample_ID:
B2-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 19:42:19 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790972
Current job name : Step_02_B2-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/8790972.1.linga

Loading required modules...


List files in scratch directory:

total 92M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:42 SRR6575964_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:42 SRR6575964_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575964_1.fastq <==
@SRR6575964.1 1/1
CNTGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575964.2 2/1
CACTCATACCTCCAGACAAAAAGCAGATACCAGGAACAGCTGCAGGAACAGTTCTGTGGAGAGCTGTGACAGTGGCCATAGCCACCTGCTCTGGTGTATA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575964.3 3/1
CTACCATCTGACTCGTGAGATGCCTCCTAGCGAAAAAACACCCTTGCAGTGTGTGATGGAGGTGGACACAGAGCGGGCCATGCTGGAGAGAGAGGCTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575964.4 4/1
ACCTTCTATAAGGCTATGATGAGCTCATGTAATTGAAACACCTGATGCTAGAAGTACTGAAGTATTAAGTAGTGGGACTTCTAGAGGGTTAAGTGGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575964.5 5/1
CATAGATAACATGGCTTCTCCATCATATCCAACCCCTACTCTGTCACTGTGGCCTGTGCCAGGCTAGGTCAGGGTAGGGGAGTGTGCACAGTACAAGCTG
+
FFFFFFFFFFFFFFF-FFFF8FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFF-FFF---FF---FFFFFFFFFFF-FFFF-FFFFFFF

==> SRR6575964_2.fastq <==
@SRR6575964.1 1/2
NAGATNAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTATACC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575964.2 2/2
GATGGCCTCTCTGAACGCTGTGCTCAGTACAAGAAAGATGGAGTTGACTTTGGGAAGTGGCGTGCTGTGTTGAGGATTGCTGACCAGTGTCCTTCCAGCC
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575964.3 3/2
ACTTAACAGTCAGCAGCCCAATCCATGTAAGATCCTTGAGGCCCTCATCTCAGCTTTGTCAGCATCCAGCTCTTCCAGCCGTTCATAGAGCTCCATGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575964.4 4/2
CCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575964.5 5/2
ATCCTGCGTATTCCTGTCTTCCTGGCCTTACTGATCAATTTTTTCATCTTTGTCCACATCATTCACCGTCGTGTGGCCAAGCTGCGTGCCCATCAGATGC
+
88FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFF-FF-FF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6575964_1.fastq

Printing command:
fastqc --outdir SRR6575964_1.fastq

Analysis complete for SRR6575964_1.fastq

Processing SRR6575964_2.fastq

Printing command:
fastqc --outdir SRR6575964_2.fastq

Analysis complete for SRR6575964_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 490M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 245M Oct 12 19:42 SRR6575964_1.fastq
-rw-r--r--   1 kkarri waxmanlab 245M Oct 12 19:42 SRR6575964_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:48 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================