-----------------------
Start of variable list:
-----------------------
Sample_ID:
C9-MAA100140-3_57_F-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 19:44:28 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791049
Current job name : Step_02_C9-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791049.1.linga

Loading required modules...


List files in scratch directory:

total 113M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:44 SRR6576006_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:44 SRR6576006_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576006_1.fastq <==
@SRR6576006.1 1/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576006.2 2/1
GATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTGGTTGGGACTGACCCTAGTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF--FF-F-F-FFFFFFFFFFFFFFFFFFFF
@SRR6576006.3 3/1
GCTTCTAATAGATCCATGAGACCTGACAAGAATACATACGAGAGAAAACGGTCTGTGTATGTTAAGAATCCATACCTGGAAGGCATGGACGAAGACATTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576006.4 4/1
CCATTATATTCCTCTTTGTTGTTCGGAGCACATTTGAGTGGGCCAATACACAGGTCACAGAGGGAGGAATTCTTCTCATACCCGGGAGCGCAGCCTTGAC
+
FFFFFFFFFFFFFFF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576006.5 5/1
GGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6576006_2.fastq <==
@SRR6576006.1 1/2
NAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576006.2 2/2
NTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTT
+
#FFFFFFFF8FFFFF-FFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF8F
@SRR6576006.3 3/2
NATTACAACGGAGCCTGGTGCAATCCCAATTCCCCCTGACGTTCCAATTCTGATGATGGTAACATCACAGCAGTGTGCATGGTGGAGTAATTTGATGAGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF
@SRR6576006.4 4/2
NTATTATGCCGTGGCTGTGGTGAAGGCATCGGACACTAGCATCACCTGGAACAACCTGAAAGGCAAGAAGTCCTGCCACACTGGGGTAGACAGAACCGCT
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6576006.5 5/2
NGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTG
+
#FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF--FFFFFFFFFF-FF-FFFF-FFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6576006_1.fastq

Printing command:
fastqc --outdir SRR6576006_1.fastq

Analysis complete for SRR6576006_1.fastq

Processing SRR6576006_2.fastq

Printing command:
fastqc --outdir SRR6576006_2.fastq

Analysis complete for SRR6576006_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 608M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:44 SRR6576006_1.fastq
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:44 SRR6576006_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:02 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================