-----------------------
Start of variable list:
-----------------------
Sample_ID:
F6-MAA100040-3_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 19:46:08 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791168
Current job name : Step_02_F6-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791168.1.linga

Loading required modules...


List files in scratch directory:

total 39M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:46 SRR6575235_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:46 SRR6575235_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575235_1.fastq <==
@SRR6575235.1 1/1
GNTGAATATCCTGTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATNTCATTAACGAAAAGGATG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575235.2 2/1
GGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCC
+
-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6575235.3 3/1
AGATCAGAGACTGCCTTGTGTGGAAGACTATCTGTCTGCAATCCTGAACCGTGTGTGTCTGCTGCATGAGAAGACCCCAGTGAGTGAGCATGTTACCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575235.4 4/1
CTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575235.5 5/1
GACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575235_2.fastq <==
@SRR6575235.1 1/2
NCTGTNTGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGC
+
#8FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8FFFFFFFFFFFFFF8FFFFF
@SRR6575235.2 2/2
GTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAA
+
F-FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFF-F-FFFFFFFFFFFFFF-FFFFFF--FFFFFFFF-FFFFFFFFF-FFF-FFFFFFFFFFFFF
@SRR6575235.3 3/2
GTCTTCAGTTGCTCCGCTGTAGCCTTGGGCTTGTGCTTCACCAGCTCAGCAAGAGCCGTTTGTTTCTTAATCTGCTTCTCCTTCTCTGGAAGTGTGCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575235.4 4/2
GGTTTGCACAACTATGTGAGGAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575235.5 5/2
GCGTTATTCCCATGACCCGCCGGGTAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575235_1.fastq

Printing command:
fastqc --outdir SRR6575235_1.fastq

Analysis complete for SRR6575235_1.fastq

Processing SRR6575235_2.fastq

Printing command:
fastqc --outdir SRR6575235_2.fastq

Analysis complete for SRR6575235_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 255M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:46 SRR6575235_1.fastq
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:46 SRR6575235_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:36 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================