-----------------------
Start of variable list:
-----------------------
Sample_ID:
F10-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 19:44:29 EDT 2018
Running on node : scc-wa2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791136
Current job name : Step_02_F10-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/8791136.1.w-long

Loading required modules...


List files in scratch directory:

total 48M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:44 SRR6575592_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:44 SRR6575592_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575592_1.fastq <==
@SRR6575592.1 1/1
CNCCAGTCTGCGCTGGTTGTGGCCCCGCCACCCTGCGGAGGTTGGTCAGATGGTTGCCCATCTTCTTGATGAGTTTCACCTCCTTATCCAGATAGTGGCT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFF
@SRR6575592.2 2/1
GNTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTTTCATGGGTGTATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTA
+
8#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575592.3 3/1
CCGTAACCATTATAGACGCTATCCACGTCGTAGGGGTCCTCCACGCAATTACCAGCAAAATTACCAGAATAGTGAGAGTGGGGAAAAGAACGAGGGATCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575592.4 4/1
GTCCTTAGGTTTTTCAATGAAGTGTTCAGAGACAGCACTCAGACCCCTGCCATTGCTCCCCAGAGCCAGCCGGCCGCCACCGACTCCTCCGTGTCTGTGC
+
F-F-F8F8F8F8FFFFF8FFFF8FF8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575592.5 5/1
CCACTAGGTCAGCAGCATAGGTGAGATTGGGGTCGGGATGGTGGCCTCCAAAATCCTCCAGGGGAACACAGTTCACAGCTGAGTTTGCAGGGGCACCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575592_2.fastq <==
@SRR6575592.1 1/2
NCCTGGTCAACTTGCACCTGCGGGCCTCCTACACCTACCTCTCTCTGGGCTTCTTTTTTGATCGGGATGACGTGGCTCTGGAGGGCGTAGGCCACTTCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-FFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-
@SRR6575592.2 2/2
NCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCACTGAGAAGTCCAATTCCAGTCTATCCACATG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575592.3 3/2
NAAAAAACCCCATGCTGCATAGATAATGCAGATAGTTCTAATGTTATCTGGTCAGAGGGCAAAAAGCAAGCACTTAAGGTCTTCAGCTCCAATCTTTGTT
+
#FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575592.4 4/2
GTCCTGATAGAGCTCAGGCAGGGTGACCCCTCTGGCTGCTGCCAGATTCCGTAGAGCACACAAGTGTCGGTCATAGCCCTGGCCCATCGCTGCGTCTTGG
+
8FFFFFFFFFFFFF8FFFF8FFFFFF8FFFFFFFFFF--FF-FF-FFF-FF--FF-FF--F--F-FFFFFF-F--F-F--FFF-FF-FFF8FF-F----8
@SRR6575592.5 5/2
ATCCAGGAGGGCCCAATGGAGATTTTGGAATTAAATTCAATATTTCTAATGGGGGTCCTGCTCCAGAAGCAATCACTGATAAAATTTTCCAAATCAGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-

Starting FASTQC command


Processing SRR6575592_1.fastq

Printing command:
fastqc --outdir SRR6575592_1.fastq

Analysis complete for SRR6575592_1.fastq

Processing SRR6575592_2.fastq

Printing command:
fastqc --outdir SRR6575592_2.fastq

Analysis complete for SRR6575592_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 261M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:44 SRR6575592_1.fastq
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:44 SRR6575592_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:44 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================