-----------------------
Start of variable list:
-----------------------
Sample_ID:
H20-MAA000377-3_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 19:46:11 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791233
Current job name : Step_02_H20-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791233.1.linga

Loading required modules...


List files in scratch directory:

total 28M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H20-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576314_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:46 SRR6576314_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576314_1.fastq <==
@SRR6576314.1 1/1
ATCTGAAACAAAGCCCACAGGATACGCCCGAGACCCTCAATTCAAGGAGAGCTCCAAGGATGTGTTGGACTCTGTGCTCCAGTGGGGCACTGGCTGCACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576314.2 2/1
CAGTTCGTCAGCTTCATCGGGAGTTCCTCAGAGCTGGATCGAACGTCATGCAGACCTTCACTTTCTATGCAAGTGAAGACAAGCTGGAAAACAGAGGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576314.3 3/1
AACCAAAGTATTTTACAGAATTTACTACAAAATGCCATAAAAACCGCTTCAACTTAAGCTCTCTCCCCCCGTATCCGGCGAGCCAACTGGATGTCTTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576314.4 4/1
GTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576314.5 5/1
AAGCTTTAGAACAAATAATTTAAACGTATCTTAAACACTGAAAAATGTGTTTTTAATTGTTATTTATAGTTAATTAACACTACCAGTGTTTAGCTTTATG
+
-8F-FFFFFFFFF8FFFFFF8FFFFFFFF8FFFF8FFFF8FFFFFFFFFF--FFFF-FF-FFF-FFFFF-FFFFFF-F--FFFFFFFF-F-FFFF-FFF-

==> SRR6576314_2.fastq <==
@SRR6576314.1 1/2
GCATAAAGGCTTGGTACTGACAGACTGCCCAGAGCCCAAGGTCCTGAGAACAGTTTTTAGAAGCCTGGGTGCCTCAGTAGGTACCTGCCCTATGTGTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576314.2 2/2
CCACACGGCTTCTTCAACATGTTCAAAATACTCTGCAATGAGGAAGTCCACGTTCTTCTTCATGAACACCTCTAGCTGTTGGCGAAATATCTTTTTCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF
@SRR6576314.3 3/2
AAGCATACCTGGTGGGGTTGTTTGAAGATACCAATCTGTGTGCCATCCACGCCAAGAGAGTCACCATCATGCCCAAAGACATCCAGTTGGCTCGCCGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF
@SRR6576314.4 4/2
CGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8FFFFFFFFFFFF
@SRR6576314.5 5/2
CTACCACTACAATGGATTGAAGCAGTCAAATTATAATGAAAAGGTAATGTAAGTGGAAGGGACTGCAGTGGTTATGGGTTTTGAAGACCCCATGCTACAG
+
FFFFFFFFFFFF8FFFF8FFFFFFFFFFF8FFFFFFF-FFFF-FFFFFFFF-FFFFFF-FFFFFFF-FFFFFFFFF-FFF-FFFF-F8FF-F-F8FFFFF

Starting FASTQC command


Processing SRR6576314_1.fastq

Printing command:
fastqc --outdir SRR6576314_1.fastq

Analysis complete for SRR6576314_1.fastq

Processing SRR6576314_2.fastq

Printing command:
fastqc --outdir SRR6576314_2.fastq

Analysis complete for SRR6576314_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 150M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H20-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  75M Oct 12 19:46 SRR6576314_1.fastq
-rw-r--r--   1 kkarri waxmanlab  75M Oct 12 19:46 SRR6576314_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:36 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================