-----------------------
Start of variable list:
-----------------------
Sample_ID:
G4-MAA100140-3_57_F-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-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791201
Current job name : Step_02_G4-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791201.1.linga

Loading required modules...


List files in scratch directory:

total 65M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6576101_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576101_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576101_1.fastq <==
@SRR6576101.1 1/1
TCACAGAACAACCGCCGCATACGGCCGATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCTAAACCGACGCAGTTTTGCTCCTTGGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFF-FFFFF
@SRR6576101.2 2/1
ATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576101.3 3/1
TTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576101.4 4/1
GCCCAGCATGGTGTGCACCTCGTTGCGGTACTGCCCGAGTCGGTTGCGTAGATCCTCCATGTCGACTCCGAGTCGGGCCTGTGCCGCCTGCACCTCTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576101.5 5/1
ATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTTGTGCGCCGGCAAAACTTTTCAGGCGAATTTCCGCCCCTGGCGCTCTAGGCTACTACGTGCGCGA
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576101_2.fastq <==
@SRR6576101.1 1/2
GCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTACCAGCTCGATAATTGGCGCAAGTTGTAGGTCGGGGGCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576101.2 2/2
CTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576101.3 3/2
ACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFF-8FF
@SRR6576101.4 4/2
GGTCCAGGAAGAGCTGCAGAGCTCCCAAGTCACACAAGAACTGACGGCACTGATGGAGGACACTATGACGGAAGTAAAGGCTTACAAAAAGGAGCTGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFF
@SRR6576101.5 5/2
GTATAGGGACGCCCCCTGCTCGCGTTACTGCCAAGCGAGCGTGGTGTGGTGCCCCCGACCTACAACTTGCGCCAATTATCGAGCTGGTAGACGACCAGCG
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6576101_1.fastq

Printing command:
fastqc --outdir SRR6576101_1.fastq

Analysis complete for SRR6576101_1.fastq

Processing SRR6576101_2.fastq

Printing command:
fastqc --outdir SRR6576101_2.fastq

Analysis complete for SRR6576101_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 378M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 189M Oct 12 19:46 SRR6576101_1.fastq
-rw-r--r--   1 kkarri waxmanlab 189M Oct 12 19:46 SRR6576101_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:31 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================