-----------------------
Start of variable list:
-----------------------
Sample_ID:
F7-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-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791173
Current job name : Step_02_F7-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/8791173.1.linga

Loading required modules...


List files in scratch directory:

total 56M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:46 SRR6575238_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:46 SRR6575238_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575238_1.fastq <==
@SRR6575238.1 1/1
ANTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATA
+
F#FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575238.2 2/1
GGGCTGCGGCGCAGTATGTCTTTCAGAGAGCCATCCTGCTCGCTCAGCAGCTTGTTGATCTCATTCTGCTTGTATTCAGGTGAGAGGCGGTGGCCGAAGC
+
FFFFFFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575238.3 3/1
AAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGGTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAA
+
FFF8FFF-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFF-FFFFF--FFFFFFFFFFFFFFF--FFFFFFF-FFFFF
@SRR6575238.4 4/1
CTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCTCCAACTAAGAACGGCCATGCACCACCA
+
8FFFFFFFFFFFFFF-FFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFF-FF-F--FFF-FFFFFFFFFFFF
@SRR6575238.5 5/1
CTTCCACAAAGAAAACACAGTCACCAATGACTGGATCCCAGAGGGGGAAGAGGATGAGGACTACCTGGACCTGGAGAAGCTGCTTGGTGAAGATGACGAC
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575238_2.fastq <==
@SRR6575238.1 1/2
NATATNCGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTA
+
#FFFF#FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575238.2 2/2
GCATTATCCTCAACGTGGCGGAGGTGGTGTACCTCATCATCCGGGCCTGTGCCCGCCGTGCTCAGCGCCGCTCCAATCCGCCCTCCCGCAAGGGCTCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575238.3 3/2
ATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATT
+
FFFFFFFFFFFFFFF-8FFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8F
@SRR6575238.4 4/2
CCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTTACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGAT
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6575238.5 5/2
GTGTAGAACTGAGTGTACTTCTTCATGGGTCTCTCCCCTCAGACCTAAGGAGATCATCCCCATGGCAGTAGAAATGCCAACAGGTGCTATGAAGAGGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575238_1.fastq

Printing command:
fastqc --outdir SRR6575238_1.fastq

Analysis complete for SRR6575238_1.fastq

Processing SRR6575238_2.fastq

Printing command:
fastqc --outdir SRR6575238_2.fastq

Analysis complete for SRR6575238_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 315M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 158M Oct 12 19:46 SRR6575238_1.fastq
-rw-r--r--   1 kkarri waxmanlab 158M Oct 12 19:46 SRR6575238_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:31 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================