-----------------------
Start of variable list:
-----------------------
Sample_ID:
D5-MAA100138-3_56_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 19:44:32 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791083
Current job name : Step_02_D5-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791083.1.linga

Loading required modules...


List files in scratch directory:

total 77M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:44 SRR6575810_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:44 SRR6575810_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575810_1.fastq <==
@SRR6575810.1 1/1
GATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575810.2 2/1
GCCCATATGCATCTGCTTTGACTGGTGGTCTCTGTCAACCTACAAAGACTGACCTATTGCTGAGGGCAGCTGGACAACTCTGAACAACTTAGAGAACTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575810.3 3/1
CACGTAGACTCTCTGCGCACACAGCTAGCGCCCCACAGCGAACAGATGCGCGAGAGCCTGGCCCAGCGCCTGGCTGAGCTCAAGAGCAACCCTACCTTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575810.4 4/1
CTCTGGGTTCAACCGTTAGTCAGCTGCAGGAACGGCTGGGCCCATTGACTCGGGACTTCTGGGATAACCTGGAGAAAGAAACAGATTGGGTGAGACAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFF-FFFFFFF
@SRR6575810.5 5/1
CACTTCATCCGGCGACTAGCACCGTGCCGGCAGTCTACAGCATGGCTTCCGTCTCCGAGCTCGCTTGCATCTACTCCGCCCTCATCCTGCACGACGACGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575810_2.fastq <==
@SRR6575810.1 1/2
NCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575810.2 2/2
GTATATAAGCCATGATGAGACCTGAACCTCCCCAGTCCTCGTTATGAAGCCAAGCTTTCAGGACTGACGGTGGCCATGCGGGTCAATGCTGAACATGGGA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF-FFFFFFF-FFF-FFFFFFFF-88FFF
@SRR6575810.3 3/2
CCAATGCGGGGGTGGGGAGTGGAAGCGGGCACCTCACTGGGCAGTCAGAGTCTCGCTGGCCTTGCCGATCACACTCTGGACTTGGGTCTTAAGCGTCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575810.4 4/2
GGGGACAGTCTCCCTTGCAGCTCCTGCAGCTTCTGGCGCGCGCTCTCCTGCAGCTCGGCGCCCAGAGGCGCCACCTTCTGGCGGTAGAGCTCCACATCCT
+
F8FFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFF8
@SRR6575810.5 5/2
ACCAGCAGGCGCAGCTCCAGCTGCTGGAGCGGGCCCACCAGCCCCTACATTGCAGATGAGGCTCCCAATGTTGACATTGGCCAGAGCCTTGGCAAACAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF--F8FFF

Starting FASTQC command


Processing SRR6575810_1.fastq

Printing command:
fastqc --outdir SRR6575810_1.fastq

Analysis complete for SRR6575810_1.fastq

Processing SRR6575810_2.fastq

Printing command:
fastqc --outdir SRR6575810_2.fastq

Analysis complete for SRR6575810_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 407M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 204M Oct 12 19:44 SRR6575810_1.fastq
-rw-r--r--   1 kkarri waxmanlab 204M Oct 12 19:44 SRR6575810_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:15 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================