-----------------------
Start of variable list:
-----------------------
Sample_ID:
C14-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 19:46:09 EDT 2018
Running on node : scc-yc2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791318
Current job name : Step_02_C14-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/8791318.1.y

Loading required modules...


List files in scratch directory:

total 51M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 C14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:46 SRR6576824_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576824_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576824_1.fastq <==
@SRR6576824.1 1/1
CCCCTATGGCCTCGTGGCTCCTCGGTTCCAGCGAAAGTTCAAGGCCAAGCAGCTCACCCCAAGGATCCTGGAAGCTCACCAAAACGTGGCCCAACTCTCA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFF
@SRR6576824.2 2/1
GGCCAGGCACAGGATCAGGGTTTTTGCCGCCAGGATATACAGCAGCAGGGGCACGTGTTCAAGAACCTTCCAGTTCATGGCGGGCCAGCTGTGATTCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576824.3 3/1
CTTCTTACCCAACCAGCTGTATGGTGCAGTATTTAATCCTTGCCCAATCCCCCTAAAGCATTACGCATATTGGATACAAGGAATCACTCTGTTTTCTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576824.4 4/1
GCTGAAGCTGAAAACGGGGAAGCTGATATCCCTCAGTGCGCAGAACCTGGTGGACTGCTCAAATGAAGAAAAGTATGGGAATAAAGGCTGTGGAGGCGGC
+
F--FF8FFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF-F--FF-FFFFFFFFFFFF
@SRR6576824.5 5/1
CTTCATTATTGCTTCATTGGACTGAAAAACCTAAGAGGCAACAGCAGTGCTCGATGGTGAAAACTAAACATGAGGGCAGCGGTGTGCCCCTAAATGTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576824_2.fastq <==
@SRR6576824.1 1/2
NTGTTCATCGAACTCAATGGCCACCTGCCGTATGTCCCAGTTGACGTTCCATTGCCGCATGTTGCTGAAGCGCCAGGTCTTGACCACGTCACCCACGGCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFF-F-FFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFF
@SRR6576824.2 2/2
GTATCAACGCAGAGTACATGGGGGGAGTCGTGGTTTGTGAGCAGCAAGCGAGGAGGCCCCGCCGCCCTGAGTATCAGAACTTCCAGCTCCTTGGGTCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576824.3 3/2
GTCATACCTTGCCTTGTCGAATTTATCCACCAGGTTTTTATTCTTGTATTCTTCTTATGATTTAAAATCTCCTTACTATGTCTTTTGAATAGTAGCCTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576824.4 4/2
GAGTTATAGTGACACTTTTCATCCGTGGCTTTGTAGGGATAGGAAGCGTCTGCCTCTATGCCCCCATTATCAATGATGTACTGGAAAGCGTCGGTCCTGT
+
FFFF8FFFFFFFFFFFFFF8F88F8FFF8FFFFFFFFF-FFFFF-FFFFF-FFF-F-FFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFF-8FF8FF-FFF
@SRR6576824.5 5/2
GTCTAATATATGATAGGATATATGATTGGATGCCTGAACAGCCAAATATATTCCAAGTGGAGCAGTTGGAGCGCCTGAAGCAAGAATTGCCAGAGCTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576824_1.fastq

Printing command:
fastqc --outdir SRR6576824_1.fastq

Analysis complete for SRR6576824_1.fastq

Processing SRR6576824_2.fastq

Printing command:
fastqc --outdir SRR6576824_2.fastq

Analysis complete for SRR6576824_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 262M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 C14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:46 SRR6576824_1.fastq
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:46 SRR6576824_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:26 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================