-----------------------
Start of variable list:
-----------------------
Sample_ID:
I9-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 19:46:10 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791261
Current job name : Step_02_I9-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/8791261.1.linga

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 I9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:46 SRR6576441_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:46 SRR6576441_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576441_1.fastq <==
@SRR6576441.1 1/1
CATCAATATATAATCTCTGATCTTCCAGGATGGAGGAGTACTCATTTATGACATTTTCATTCTCTTTAACTTGAGCTTGCTTCTTTTTCCACATGTCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576441.2 2/1
CGCTAAGAGCGACTACGAAACCTTTGTGCCGCTGGCGAGCCATCCATCGGCCAGAAAGTCGGACGGCGCCTGATTTCAGGGCCGACAGCAATCGGTCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576441.3 3/1
GGAGAAAATTGTTAGGTCTACTGATGCTCCTGCATGGGCTAGATTTCCGGCTAGAGGTGGGTAGACTGTTCATCCTGTTCCTGCTCCTGCTTCTACTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576441.4 4/1
TTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576441.5 5/1
GTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF

==> SRR6576441_2.fastq <==
@SRR6576441.1 1/2
ATCTATGGCTGCTGCTGCTATTGTGTGTTTTCTCAGTTCAAACTCAAGCTGCCGATGATGACTACGATGAACCGACGGATAGCTTGGATGCCCGTGGTCA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576441.2 2/2
CAGTAGCCTGGCGCCAGCGGCAAGAGCGGGCGACGAAGAGCCGCGCCAAGCCGAAGAGGCGAGTTCGAGCAAGCTCGCCCCAGTGTCGAGAAGCTCTCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576441.3 3/2
TCTATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAGGTGCACTTTTAGGAGATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF-FFF8F-FFFFFFFFF-888
@SRR6576441.4 4/2
AATGAAAACATTCTTGGCAAACGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF-FFFFF-FF-8FFF8
@SRR6576441.5 5/2
CAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCG
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576441_1.fastq

Printing command:
fastqc --outdir SRR6576441_1.fastq

Analysis complete for SRR6576441_1.fastq

Processing SRR6576441_2.fastq

Printing command:
fastqc --outdir SRR6576441_2.fastq

Analysis complete for SRR6576441_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 146M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 I9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  73M Oct 12 19:46 SRR6576441_1.fastq
-rw-r--r--   1 kkarri waxmanlab  73M Oct 12 19:46 SRR6576441_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:25 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================