-----------------------
Start of variable list:
-----------------------
Sample_ID:
O6-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 19:49:49 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791357
Current job name : Step_02_O6-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/8791357.1.linga

Loading required modules...


List files in scratch directory:

total 20M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 O6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.5M Oct 12 19:49 SRR6576698_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.8M Oct 12 19:49 SRR6576698_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576698_1.fastq <==
@SRR6576698.1 1/1
ATAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAATATGCGTTTATAACTGTCTATTAAAAACAAAACCGAGCCCACGATACCGCAATTAAACGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8F88-F8--FF---F--------F---F-F-F-F--F---FF--------F------FF-----
@SRR6576698.2 2/1
TGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-
@SRR6576698.3 3/1
TGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576698.4 4/1
ACGATACTGATATTACTTCTCGTTTTGAAGCAAAGGCCTCTCAAATTATAAAGATCATGATGAGAACAGCTGTTAGTGAAATAAATGATCCTATAGAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFF---FFF-FFFFF-FF-FFFFFFF-FFFFF-FFFFFFFFFFFFFF
@SRR6576698.5 5/1
CTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576698_2.fastq <==
@SRR6576698.1 1/2
NTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTATATTTGAATTTAAACAAAATGACGCAGCCGACCATAGCCCAAGTGGTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-------------F---FF------F--F8-F-------F-----8----
@SRR6576698.2 2/2
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCTTTAAATCAGTTATGGTTCCTTTGGTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFF-FFFF--FFFFF-FFFFFFFFF-F-FFFFFFFF-FFFFFF
@SRR6576698.3 3/2
ATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576698.4 4/2
TTACTAAACACCTAACAGACCGCAACCTAAACACAACTTACTTAGATCCCCCTCGAGGAGGGGACCCAATTCACTACAAGCATCTGTTCTGAATCTTTAG
+
--FFFF-FF88FFF8-FFFFF8F8-FFFFFFFFFFFF-F----FFFFFFFF-F---FF-F---FFFF--FFF--FFF-F-F-FF--FF-FF8FFF--F--
@SRR6576698.5 5/2
AAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6576698_1.fastq

Printing command:
fastqc --outdir SRR6576698_1.fastq

Analysis complete for SRR6576698_1.fastq

Processing SRR6576698_2.fastq

Printing command:
fastqc --outdir SRR6576698_2.fastq

Analysis complete for SRR6576698_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 109M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 O6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:49 SRR6576698_1.fastq
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:49 SRR6576698_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:11 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================