-----------------------
Start of variable list:
-----------------------
Sample_ID:
D17-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-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790751
Current job name : Step_02_D17-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/8790751.1.linga

Loading required modules...


List files in scratch directory:

total 48M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 D17-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  24M Oct 12 19:41 SRR6576252_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  24M Oct 12 19:41 SRR6576252_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576252_1.fastq <==
@SRR6576252.1 1/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGTCTATTAAACACATCTCCGAGCCCACGAGACATGACGTAATAGGGTTTGGCGAGTGAGGCTTGTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8F8FF888FF-F-F-F---FF-F-FFFFF----FF----------F-F-------------F-----F-
@SRR6576252.2 2/1
GTTCATCGTCACACAAACAAGTGCTGGTTTCAGATACAGCTGGATTATGCAGGGACTGCTTGGATAGAAGTCTGTTATATTAAAATTTTTTTCAGAATAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576252.3 3/1
GAGTGCGGCCTCCCCCGTCCCCGCGGCCGTCCATCGTGGAGCCGGGCTGGTGATTCTAGCGGGGGAGGGTAGCGTGGCGCGGCGGCAGGGGGGCAGGGGG
+
F8F-FFFF-FFFFFFFFFFFFFF8F88FFFFF888-8FF8F-8FFF------F---------FFF-F---------F---F--F----F-F---------
@SRR6576252.4 4/1
TTTTAGTACTGTGTCTCCAGGCTGCCTGAGGCCTCAGCTGTTGTCATTCGTGCTGTGTGGGGGTGACATTTCTGCCTGTAGTGAAGATCCTTCTCAGTGG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576252.5 5/1
GTTATATACAACCCAACACGGTGTGTTTCTGGGACCGACGACTGGCGGTGTCCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576252_2.fastq <==
@SRR6576252.1 1/2
NCAAAAAAAAAAAAAAAAAAAAAAAAATTACCTGTCGCTTAAAAAAATCTGACGGGGCCGCCGATTCCTGGTGTGTATTGATTGGTGGTGGGGGGTTGAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFF--FFF--------FF-F-F---F----F--FFF--FF------F--------F-----F-F--F-F--------
@SRR6576252.2 2/2
GCTCACAGAACTTAAGCCGAAGACTGTTGTTGAAAGTACACATCTCTCTTCAGTCTCTACCATGATAGCAGCATCAGATGTTTTCATTAACCAAGAAAAC
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-F-FFFF8FFF
@SRR6576252.3 3/2
GGGCTACATTCTTCAAGGCCTCATGCAGGACGGCTGGCGGGTGGGGGTGGACGGCACGCATCTCGCACTCTATCTGCGGGGTGAAGACTCGGGTGCCTCA
+
--------F8FFFF8F8F-88FFF--FFF---F-----FFF-F-F-F-F--F--F-FF----F--FFF----F-FFF-FF-F------------------
@SRR6576252.4 4/2
CCCATGTGGAGACTACACAAGCTGATTCACACGGTCACACAGCCGTGGAGACAAATATCTTCCTTAATAGAGAAAGACAGACCAGAGATGACAATTAGCA
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-F
@SRR6576252.5 5/2
CATATCTAACAGGGAAGAGGAAATGGGAGGGAGATGAGAAAACAGGATGGTACCAATCACCTGGGTAATCAACTGGTTGAAGAGGCTGCAAGGAGAGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576252_1.fastq

Printing command:
fastqc --outdir SRR6576252_1.fastq

Analysis complete for SRR6576252_1.fastq

Processing SRR6576252_2.fastq

Printing command:
fastqc --outdir SRR6576252_2.fastq

Analysis complete for SRR6576252_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 240M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 D17-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 120M Oct 12 19:41 SRR6576252_1.fastq
-rw-r--r--    1 kkarri waxmanlab 120M Oct 12 19:41 SRR6576252_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:57 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================