-----------------------
Start of variable list:
-----------------------
Sample_ID:
F16-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 19:41:27 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790776
Current job name : Step_02_F16-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/8790776.1.linga

Loading required modules...


List files in scratch directory:

total 37M
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 F16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576036_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576036_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576036_1.fastq <==
@SRR6576036.1 1/1
GGTCTAGAGGGACCGAAGCCAGTGAGTACAACACGCACCTAGATCACAGGGTTGACCTGAGTCTGTATTCTTGCTCCCAGCCCAGCGCCTAGCTCCTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576036.2 2/1
CCTAATGCTGTGACCCTTCAATACAGTTCCTCATGTTGGAGGTGACCCCCAACCATAAAGTTATTTTCTTTGCTACCTCATAGCTGTATTTTTCTACTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576036.3 3/1
GTTATTATCCTAGTATCCTTGGTCTATCTCAAGAAAAAGCAGGTTCCAGACAATCCTCCTGATCTGGAAGAAGCTGCCAAAACTGAGGCTGAGAATACGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576036.4 4/1
GGTCCTCCTCGTCACCCTGAATGGTCTTCTTTATGCGCAGAAGCATGGTGGTAAGCCACTGGTCCAGTCTGGAGATGGAGTCATATTCCTTCACCGCCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576036.5 5/1
GCCCTGGCCAGGCTCGGTGTGTATGGAGCCCTGGTCCTCACAGTGTTCGTCCCTCTGCCTCTCCTCCTTGCCCAGTACAACAGAGATGAGGGAGAGTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576036_2.fastq <==
@SRR6576036.1 1/2
CTGCTGGAGCCAACTCCCTCTGCCACCTCCCATGACCCTGCGCAGCTCCTGTTATCTTTCTGCCTTTCTGTTTGTCCATTCTTTGACACTGGTAGTTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576036.2 2/2
GTACATATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAA
+
F-FF88888888F8F8F8F88FF8FFF8FFFFFFF8FFF-FFFFFFFF-FFF-FF-FFFFFFFFFFFFFF-F---FF-FFFF-F-FFF-FFFF-----F-
@SRR6576036.3 3/2
CTGGTAATCATGCTCTGTTTCTTCATCCAGGGCTTCGGGATGCTTGAGAAGTGAGTAGGTGATCGTATTCTCAGCCTCAGTTTTGGCAGCTTCTTCCAGA
+
FFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-8FFFF8
@SRR6576036.4 4/2
CTCAAGTACAGCGCCAAAGACTACTTCTTCAAGGCGGCCCTCTGCCACTTCTGCATTGACATGCTCAACGCCAAGCTCGCTGTTCAGAAGTATGAGGAGC
+
FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576036.5 5/2
CCACAGCCCGTCTGCACAGTGAGTGGTCCCCTCTGCTGTGCTGGAGATCAACATTAGCTATGACACAGGGTGACTGAGAAGAACTACTCAGCACAGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576036_1.fastq

Printing command:
fastqc --outdir SRR6576036_1.fastq

Analysis complete for SRR6576036_1.fastq

Processing SRR6576036_2.fastq

Printing command:
fastqc --outdir SRR6576036_2.fastq

Analysis complete for SRR6576036_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 188M
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 F16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  94M Oct 12 19:41 SRR6576036_1.fastq
-rw-r--r--   1 kkarri waxmanlab  94M Oct 12 19:41 SRR6576036_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================