-----------------------
Start of variable list:
-----------------------
Sample_ID:
A6-MAA100042-3_9_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 19:42:19 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790939
Current job name : Step_02_A6-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790939.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 28 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:42 SRR6575527_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:42 SRR6575527_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575527_1.fastq <==
@SRR6575527.1 1/1
ANGCAGAGTACATGGGGACCCTGTTGACCCACTTCCAGGACCTCACTCCCTCTTGCCAGGAAGAGCTATCCCCAACAACAGNTTTCCCTTCAGACCCGGC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575527.2 2/1
GCAAAAGGAAATGGAAGATAAAGTAACTAGTCCAGAGAAAGCTGAAGAAGCAAAGTTAAAGGCAAGGTATCCTCACTTGGGACAAAAGCCTGGAGGGTCT
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF
@SRR6575527.3 3/1
CACCAATTCCTTAGAGATGTAATAGCCCATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAGGAAGAAATATGACAAGGAGTAGTAGT
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFF
@SRR6575527.4 4/1
CACTAGAGCGACACCAACATCGTTACGCTTACACACCGGACGCTTGGATCAGTGGGAAGTGCTCACGCGCGGAGCCCACTGGGCGAACAGCAACGTTATA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575527.5 5/1
CGGCCTGGGAGATCGTTTTAAGATCGAGGGACGTGCGGTTGTTCCGGGGGTGAAGCCTCAGGACTGGATCTCCGCGGCCCGAGTGCTGGTAGACGGAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFF

==> SRR6575527_2.fastq <==
@SRR6575527.1 1/2
NACCTNTTCCCAANCTGACCCCTCTTTGAGCAACCTTGTCCTTGGTGCCCACAGAACCAGAAACCGACAGCAGAGATCAGCATCCAAGGAAACAGCATCC
+
#FFFF#FFFFFFF#FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575527.2 2/2
NCGCTGAGGGAGGTCCTGTGGAGTGGGAATGTGGTCACCAGTGACCTCTGTCTTATCCGGGGCTGCAGCAGGAAGCTGCTTGTTCTTCATCTTTGCTTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575527.3 3/2
ATATGGAATCATTGGAGTGCCAGTAATTCTACCACGCCTTATATTTAAAGACAAAAAGAAGTGTCTAACAACAACATCCACACTACTACTCCTTGTCATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575527.4 4/2
GCCCTATTACGAGGGTTGTAGTCGTGTGGCACCAGCGCGGCTACTCCGATAGCGACTGGACACAACATGGCAGTTGGCCCACATGGAATATCGGTTTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575527.5 5/2
CATCAGGCAATTCATGGTTGGAATTCAACATGTTCATTGACTGCTCCATCTCCCGTCTCATGTCAGGATCACTTGTGTTCACCACTTTAGGCAGAAGCAC
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF-FF8FFFFFF8-

Starting FASTQC command


Processing SRR6575527_1.fastq

Printing command:
fastqc --outdir SRR6575527_1.fastq

Analysis complete for SRR6575527_1.fastq

Processing SRR6575527_2.fastq

Printing command:
fastqc --outdir SRR6575527_2.fastq

Analysis complete for SRR6575527_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 321M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 28 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:42 SRR6575527_1.fastq
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:42 SRR6575527_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================