-----------------------
Start of variable list:
-----------------------
Sample_ID:
N7-MAA000907-3_11_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 19:42:17 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790878
Current job name : Step_02_N7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790878.1.linga

Loading required modules...


List files in scratch directory:

total 31M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6576652_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6576652_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576652_1.fastq <==
@SRR6576652.1 1/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTAAAAACAAACTGAGATAAAATTTATTTTTAATAGTTAAAAAAATTTTTATAAACCATTTTTATAA
+
FFF8FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-8F88-F8F-------F-F-FF--FFFF--------FF--FFFFF--F-F-FF-FFF-----FFF
@SRR6576652.2 2/1
TGCTATCATCAACAGTGGCCCCCGAGAAGACTCAACACGCATTGGGTGGGCCGGTACAGTGAGACGACAGGCTGTGGATGTGTCCCCACTGCGTCGAGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576652.3 3/1
GTCAAAACCGCGCAATTATCCCCGTCCTGATTTACTGGACTCGCAACGTGGGTCCATCAGTTGTCCGTATACCAAGACGTCTAAGGGCGGTGTACACCCT
+
8FFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576652.4 4/1
GTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576652.5 5/1
ATCGTGGTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAGTAATTCCTGGAGGAATAGGTACCAAGAAAAAAACGAACCTTTGGGTTCCAGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576652_2.fastq <==
@SRR6576652.1 1/2
GGCTATGAAGGAACAGATTCAAATAAGAATAAATATTGGCTTGTCAAGAACAGCTGGGGAAGTGAATGGGGTATGGAAGGCTACATCAAAATAGCCAAAG
+
--FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-F-FFF-FFFFFFFF-FF--FF-FFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576652.2 2/2
GTTCCAAAGGACACAGTTTATTAGGCAGCAGCTGGGAAATCAGCGGTTAGACTTGGCCACACGCTCCAGTTCATCTTTCTTCTTGATGGCATAGGAATTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6576652.3 3/2
GCCACGAGTCACGGGGTCTAACGCCTACCAGTACTGATTGCCGAGCAAATCTGTGAATGGCGACTATGCGCCTAGTCAACCAGATGTGTGCTAGCCCGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576652.4 4/2
GTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCAT
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576652.5 5/2
CAGGACCCAAAAGGCTGAAAGGGGGCAGTGAAGTCGGACGGACTCAACGCCCCTCTTTACAGCAAATACCAGCGGCCCTGACCCCGGGGAACAGTCGCAT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576652_1.fastq

Printing command:
fastqc --outdir SRR6576652_1.fastq

Analysis complete for SRR6576652_1.fastq

Processing SRR6576652_2.fastq

Printing command:
fastqc --outdir SRR6576652_2.fastq

Analysis complete for SRR6576652_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 157M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:42 SRR6576652_1.fastq
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:42 SRR6576652_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:40 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================