-----------------------
Start of variable list:
-----------------------
Sample_ID:
B10-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 19:41:26 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790720
Current job name : Step_02_B10-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/8790720.1.linga

Loading required modules...


List files in scratch directory:

total 28M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 91 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576380_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576380_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576380_1.fastq <==
@SRR6576380.1 1/1
TNGTTGATATGGTCCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCTGACTACCCTCCACTTGGTCGCTTTGCTGTTCGTGACATGAGGCAGACAGTTGC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.2 2/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.3 3/1
GGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.4 4/1
GCTAAAATAAATAAAATCCCTAGGTTTAAATTAATTAATGGGTGTGGTATTGGTAGGGGAACTCATAGACTTAATGCTAGTGTGAGTGATAGGGTAGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.5 5/1
GACCGGAGGACCCTGCAGATTCTCCGGGAAAACCTGGAGGAGGAAGCCATCATCATGAAGGATGTGCCCAACCGGAAGGTGGGCGAGTCTGTGTTCCATA
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576380_2.fastq <==
@SRR6576380.1 1/2
NTTCCACCACTGATTAAGACTGGGGTGGCAGGTGTTAGGGGTAATATTCATTTAGCCTTCTGAGCTTTCTGGGCAGACTTGGTGACTTTGCCAGCTCCAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.2 2/2
CCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF
@SRR6576380.3 3/2
TCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTTCCTCTCCGGAATCGAACCCTG
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8FFF
@SRR6576380.4 4/2
CCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATTGCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576380.5 5/2
ACATTTTATTTGACCACTCTTTATTATGTGCGTTGGCTCAGGCCCTAAGTGTACCAGGTGAAGCCGAAGTTGGCATTGCTCATCTCCTCCTTGGTGCGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFF-FFFFFF8F

Starting FASTQC command


Processing SRR6576380_1.fastq

Printing command:
fastqc --outdir SRR6576380_1.fastq

Analysis complete for SRR6576380_1.fastq

Processing SRR6576380_2.fastq

Printing command:
fastqc --outdir SRR6576380_2.fastq

Analysis complete for SRR6576380_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 156M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:41 SRR6576380_1.fastq
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:41 SRR6576380_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:52 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================