-----------------------
Start of variable list:
-----------------------
Sample_ID:
F4-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 : 8791375
Current job name : Step_02_F4-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/8791375.1.linga

Loading required modules...


List files in scratch directory:

total 41M
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 F4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:49 SRR6576315_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:49 SRR6576315_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576315_1.fastq <==
@SRR6576315.1 1/1
TNTCAACGCAGAGTACATGGGGAGATTGTCCCTGGTCCCTGTCGGCTTTACAGGGGGCTGCGGTGCTGAGGATGAGTGGGGNAGGGGAGAACCCGGCCAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576315.2 2/1
CTTCGAGGCCTGCTCGTTGAACAACAGGTGCGGTGCGTCGCCGGCGTAGCCGGCCGGGCTGTCGTGAACCGAGCCTGCGCCTGATGGCTTGTCTCGGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.3 3/1
ACCTGTTGAAACAGCTAAAAAAAGAGACTGTGTTTCATACTCCTCCACCGACCAGTGCAAAACAAGCTAAAAAGTTCCTGGGCACTGCGGGCTTTTGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.4 4/1
GGTGTGTGGAGAGCCGCGCCCGTATCTCCTCTGTGCTCTGGCCCAGCATGGTGTGCACCTCGTTGCGGTACTGCCCGAGTCGGTTGCGTAGATCCTCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.5 5/1
AGATAAGAGTAACACATTTCCCGAAACAGTGGAGTGCAGACACATCTCAGAGGCAGCTACGCAGGCACATAATTCAGAGTGTAAAAAAGGTGAAGGGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFF-

==> SRR6576315_2.fastq <==
@SRR6576315.1 1/2
NTCTCNCATTGGTGCATTAGCTGAACCAAGGAGTCCCCGATAAAGACTACTTCGGGTTCCTTGTCTTTGCTGTCCGCTACAAACCGATGGTGCAGAGACA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576315.2 2/2
NCGCGGAAGCTAGCGCCGCGGCAGGCCTCGCCTTCATGGGCAAGGGCCGGCCGCGGTTGACCGGTGTGCATATGGGTGGGGAGCTGCAAGCGCAGCGCTC
+
#FFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.3 3/2
GTGTAGACTTTTCTTTTACCATTTATAGAGCTTGTATTAAAGCCACAAGTTTAGCTTTCTGGGCTGAAGTCCCTTTAGGGAGGCTGCTGGCCTAGATCAC
+
FFFFFFFFFF8FFFFFFFFFF8FFFFF-FFF-F-FFFFFFFFFFFFFFFFFFF--FFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.4 4/2
ACACTATGACGGAAGTAAAGGCTTACAAAAAGGAGCTGGAGGAACAGCTGGGTCCAGTGGCGGAGGAGACACGGGCCAGGCTGGGCAAAGAGGTGCAGGC
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576315.5 5/2
GTATCAACGCAGAGTACAAGGGGGACACTTCCGGGTGGGACGAGAGCGAGGCTCCGGACCGATTCGGCTGCTGGGGCGCAGGCATCGCATACCACGGCCT
+
F8FFFFFF-FFF8FFFFF-FFFFFFFFF---FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF--FFFFFF-FFFFFFFF8FFFFF--FFF--FF8FFFFF

Starting FASTQC command


Processing SRR6576315_1.fastq

Printing command:
fastqc --outdir SRR6576315_1.fastq

Analysis complete for SRR6576315_1.fastq

Processing SRR6576315_2.fastq

Printing command:
fastqc --outdir SRR6576315_2.fastq

Analysis complete for SRR6576315_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 217M
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 F4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 109M Oct 12 19:49 SRR6576315_1.fastq
-rw-r--r--   1 kkarri waxmanlab 109M Oct 12 19:49 SRR6576315_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:17 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================