-----------------------
Start of variable list:
-----------------------
Sample_ID:
K3-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 19:41:27 EDT 2018
Running on node : scc-wa2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790838
Current job name : Step_02_K3-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/8790838.1.w-long

Loading required modules...


List files in scratch directory:

total 19M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.5M Oct 12 19:41 SRR6576508_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.2M Oct 12 19:41 SRR6576508_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576508_1.fastq <==
@SRR6576508.1 1/1
TATCAACGCAGAGTACATGGGATCTGCCAAGCCGGGAGGGAAGCCTGTGCCTGCAGCTGACTCGCTCCAGTGCTGATGGGAATCCTGCCGTTCCTACTGA
+
8FFF-FFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFF8FF-FFFFFFFFFFFFFFFFFFF-FFFFFFF--FFFFFFFFFFFFFFFFFFFFFF--FFFFF
@SRR6576508.2 2/1
GGAGTCCTGAAGGACTACACCGGAGAGGATGTGACTCCAGAGAATTTCCTCGCCGTGCTGAGAGGTGACGCAGAAGCTGTGAAGGGCACAGGGTCTGGAC
+
8F-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFF--FFFFF-FFFFF--FFF-
@SRR6576508.3 3/1
TCCTGCTGGCGCTGCTGCAGCGCGAGCGCACGGGCGAGTGGCAGTAGATCTCGGTGTCGCTCTACAACTCCATGCTGGCCATGCAGATGCAGGAGGCGGC
+
FF-FFF-FFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFF-FF-FFFFFFFFFFF-FFFFFFFFFFFFFFFF---FF-F-F-F-F-FFFFFFFFFFFFF
@SRR6576508.4 4/1
ATCTTATGGTGTGCTAGACATTGGCAAATGCAAAGAAGGAAAGCCTGTGTATATTTCGCTTCCACATTTCCTACATGCAAGTCCAGATGTTTCAGAACCT
+
88--FFFFFFFFFFFF-FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--FFFF-FFFFFF-FFFFFFFFFFFFFFFFF--FFFFFFFF
@SRR6576508.5 5/1
CGGCAGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTGAAAGGAATT
+
-FFFFFFFFFFFF-FFFFFFFFFFF8FFFF8FF8FFFFFFFF8F-FF-F-F-FFFF--FFFFFFFFFFFFF-FFFFFFF-FF-FFFFFF--FF-FF---F

==> SRR6576508_2.fastq <==
@SRR6576508.1 1/2
GGCCTTAAACGTGTAGCTGGCTTGGACCTGGCTCCGGATGGACCTCCCATTGTGGAACCACTGGGTAGAAGAGTTCCCAGGGTTGTGGGTCCCTTCGCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFFF8FFFFFFFFFFF8FFF
@SRR6576508.2 2/2
GTTCCCATATTGCATGACATGGCTGGTGTTGGTGTGGGACTTGACCAGGTGGTACTGCTTGTGAAGGGTCTCTTTGGTCAGGTCCTCCACATCGTAGTCT
+
FFFFFFFFFFFFFFFFF-FFFFF8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--FFFFFFFFFFFF-F-FFFF8
@SRR6576508.3 3/2
GCCCAGCGCGGTGCAGATGTCGCGCAGCGGGTTGGCCTTGAAGGCGCCCACCAGCACCAGCGGCCCGGTCCGCGTGTCGAACACGCCAGACAGCGGCATG
+
-8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576508.4 4/2
CACAATATGAAATCATAAAAGCAACAAACATCACCACTCCAATCCCAAGTAAGGCCATCTCAACCATGCCAAGGAGCTTGATATTCCCAGACACTAGTGT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-F-FFFFFFFFFFFFFFF---FFFFFF-FFF--FFF--FFFFF--FF-F-FFFF-F---F-FFFF-8FFF
@SRR6576508.5 5/2
GCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACTCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFF-FFFF-FFF-FFFFFFFFFFFFFFF-FFF-F-FFFFFFF-FFF-FFFF-FFFF

Starting FASTQC command


Processing SRR6576508_1.fastq

Printing command:
fastqc --outdir SRR6576508_1.fastq

Analysis complete for SRR6576508_1.fastq

Processing SRR6576508_2.fastq

Printing command:
fastqc --outdir SRR6576508_2.fastq

Analysis complete for SRR6576508_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 82M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:41 SRR6576508_1.fastq
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:41 SRR6576508_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:37 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================