-----------------------
Start of variable list:
-----------------------
Sample_ID:
D8-MAA100039-3_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 19:44:31 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791091
Current job name : Step_02_D8-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791091.1.linga

Loading required modules...


List files in scratch directory:

total 103M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  50M Oct 12 19:44 SRR6576881_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  53M Oct 12 19:44 SRR6576881_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576881_1.fastq <==
@SRR6576881.1 1/1
ANGCAGAGTACATGGGGGGAGTGTAGGCACTATAACCTGAAAGACGTGGTCCTGACAGGAGGACAATTCTATTCCCTANCANAATGAAGCTGCTGCTGCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6576881.2 2/1
GTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFF---FFFFFFFFFFF-FF-FFFFFFF-FFFFFFFF--FF
@SRR6576881.3 3/1
TNCATAGACTCAACGGTCAGCTGACCCCAAAGGCTCAGGGCTTCTGTGGGAAGCCAGAGGCATTAGTGAAGTGGTAAAGGCTCTGAGGTTGCTTTCCCCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576881.4 4/1
GNCTTGTTCTAGTTTTTTCACAGCCTCAACTATCTTTCCTTGGGTTCCCTTCTCCACAAAATCATTAATCACTTTCTTGGCNTCCTCTGACTCTGCAAAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576881.5 5/1
GTGTGAGGTTAGCCAGCTGGGACACCCAGTTGAACTGGTCGTTCAGCTGCTCCAGCAGGGATGAGGTGTTGAGCATCTTCGACTGGAAGGACTGCAGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576881_2.fastq <==
@SRR6576881.1 1/2
NTCTTNAGTANACNAAATGTATTGAATCCATCATAGTTCATATAATATATGCCAGCCTTTTCTGTTTGTTCACCAATCGCAGTCATTTCGGTGCACTCTT
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576881.2 2/2
NTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFF--FFFF-FFFFFFF-FFFF-F-F-FFFFFFFFFFFFFF
@SRR6576881.3 3/2
NTCTTCCCCTCCAGCTGAAGACTTGAGCGCCCTGGCCTCTGCCAACTACGAGCCATCTTGGGCATTCCTGAGGGTCTTCTCCCTCCTTGGTGGGTTTTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFF-FFFFFFFFFF8F-FF-
@SRR6576881.4 4/2
NCCAANACCTCCTCCAAACCCTCAACAGACCAGACAGTGAGCTGCAGCTGAGCACAGGCAATGGCCTCTTTGTCAACAATGACCTGAAGCTGGTGGAGAA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576881.5 5/2
NTGGATGCCATGCAGGACAGCTTTGCTCGGGCATCTGGCATCATAGACACGCTCTTTCAGGACCGGTTCTTCGCCCGTGAGCTTCATGACCCCCACTACT
+
#FFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFF-8F-FF

Starting FASTQC command


Processing SRR6576881_1.fastq

Printing command:
fastqc --outdir SRR6576881_1.fastq

Analysis complete for SRR6576881_1.fastq

Processing SRR6576881_2.fastq

Printing command:
fastqc --outdir SRR6576881_2.fastq

Analysis complete for SRR6576881_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 606M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 D8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 303M Oct 12 19:44 SRR6576881_1.fastq
-rw-r--r--    1 kkarri waxmanlab 303M Oct 12 19:44 SRR6576881_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:24 EDT 2018
0 hours, 0 minutes and 53 seconds elapsed.
==========================================================