-----------------------
Start of variable list:
-----------------------
Sample_ID:
C1-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 19:44:29 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791016
Current job name : Step_02_C1-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/8791016.1.linga

Loading required modules...


List files in scratch directory:

total 102M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  50M Oct 12 19:44 SRR6576839_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  53M Oct 12 19:44 SRR6576839_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576839_1.fastq <==
@SRR6576839.1 1/1
CNCGCGCCCTGCTCCCCTCCCGGCCCGCGCACCCGCCCGGGGTCCGGAGAGGAGGTCCGGGTCTCACCGTGCGCCGCCCCCNGGCTCACACTCCATGAGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFF-FFFFFF
@SRR6576839.2 2/1
CCCGCGCCCTGCTCCCCTCCCGGCCCGCGCACCCGCCCGGGGTCCGGAGAGGAGGTCCGGGTCTCACCGTGCGCCGCCCCCAGGCTCACACTCCATGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576839.3 3/1
GTCTGTGTCCATGCAGAAGAAGCTAGTTCTATGGAAAGGAACTTTAATGTAGAAAAGATAAATGGGGAATGGTATACTATTATGCTGGCCACAGACAAAA
+
-FFFF-FFFFFFFFFFFF8FFFFFFFF8FFF8FFFFFFFFF-FFFF-FFFF-FFFFFFF-FFFFF-FFFF-FFFFF-FFFFF--FF-F-FFF-FFFFFFF
@SRR6576839.4 4/1
CGATAACATTGTAAATTTGGTCATCTCCTAAAAGTGCACCTGGTTGACCTAATTCTGCTCGAATTAAAATACTTAGTGCAGTACCCACTATTCCCGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576839.5 5/1
GTATTAAGTTTTTCAAGATTTTAGGATACAGGGTCAATATAAAAGGTTTAGTTGTATTTGTCTATATTAACAAGACACTGGAAATTTAAAGTTAAAAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576839_2.fastq <==
@SRR6576839.1 1/2
NGTTGNAGTAGCCGAGCAGGGTCCTCAGGCTCACATGGAAACTCTGCTCATTGCCCTTGGCTCTCTGTGTCTCCCGCTCCCAATACTCCGGCCCCTCCTG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576839.2 2/2
NGTTGTAGTAGCCGAGCAGGGTCCTCAGGCTCACATGGAAACTCTGCTCATTGCCCTTGGCTCTCTGTGTCTCCCGCTCCCAATACTCCGGCCCCTCCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576839.3 3/2
NATCTGGTTCTCGGCCATAGAGCTCCATCAGCTGGAAGGTTTCTCCATCCTTTTTGTTAATGAGATGAATCATAATATAATTATCATAGTCTGTCTTAAG
+
#FF-FFFFFFFFFFF-FFFFFFFF--FFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF
@SRR6576839.4 4/2
NTTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576839.5 5/2
AGTTTTGAGTGGGCAGTTCTTGCATTCATTTTGTTTAAAATATCCCTAGATATTTCACATTTCTGTTATTGTAAATTATATTTTTAACTTTAAATTTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFF

Starting FASTQC command


Processing SRR6576839_1.fastq

Printing command:
fastqc --outdir SRR6576839_1.fastq

Analysis complete for SRR6576839_1.fastq

Processing SRR6576839_2.fastq

Printing command:
fastqc --outdir SRR6576839_2.fastq

Analysis complete for SRR6576839_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 586M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 293M Oct 12 19:44 SRR6576839_1.fastq
-rw-r--r--    1 kkarri waxmanlab 293M Oct 12 19:44 SRR6576839_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:23 EDT 2018
0 hours, 0 minutes and 54 seconds elapsed.
==========================================================