-----------------------
Start of variable list:
-----------------------
Sample_ID:
D12-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 19:41:27 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790748
Current job name : Step_02_D12-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/8790748.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6575259_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6575259_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575259_1.fastq <==
@SRR6575259.1 1/1
GGTACTTGAGTTGGCAGGAAATGCGTCAAAAGACTTAAAGGTAAAGCGTATCACCCCTCGTCACTTGCAGCTTGCTATACGTGGAGATGAAGAATTGGAT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575259.2 2/1
GTGGAACACTTACTGGATGAGGTCAGATCCTGGATGGCAGCAAAAGGCTTAATAACTAAACATTCATCCTCTAAAATGGATCAAAGCTGAGCCAACTGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575259.3 3/1
TGACTGGGAGGAGATTGTGAAGACCTTTGAGATTTCGGAGCCTGTGATCCCGCTGAGTCAGAGCCAGCAGCGGCTCAGTGCCTGATGCCAGCAGCGGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575259.4 4/1
CTCCTATAATGATCACCTTTATCATTTGTAATGTGTGTTACAGTGTGACAGTACAGTGTCTGTTCTGAAATGCTTCATTTTGTTACTTAAAATACACAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575259.5 5/1
CTGCCATACCGGTATATTACCTACGGGATGGTTGGGTTCTCCATCACGTTTTTGGTCCCCTATGTATTTTCCTTTATTGGTATCTCTTGATGGAGGAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFF-FFFFFFFFFF-FF

==> SRR6575259_2.fastq <==
@SRR6575259.1 1/2
NAGTAACACTTAAATATGGTTAAGACTCGAATGCAGAAATTTGGTTGGTTGGAAGGCTAATTAAGCCTCCAACTTGCTCAAATAGAATTACAAAAAGGCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8-888F-F
@SRR6575259.2 2/2
NATCTGTTATGACTAAGGCCCTTTCCCTCCTCCTTTCTTGTACTGATGCCTTCTTGTCTGTCTTCCTGCCGTGCTTGGGAAACACTTCTCAAGCTAAATG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575259.3 3/2
TGGCAGTGGATTTCCTTTAATCAAAGACAACCATGACAGATCCAATAACTATCAAAAGCTACATTTTACCAAAAACAAATCTTCATCTTTAAAAACATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFF-F-FFFF-F-FFFFFFFFFFFFFFFFF8FFFFFF
@SRR6575259.4 4/2
GAGCACGTCCCTGTAACTGAAAGTAGAACTCTGCTTTGCTTTGAACTGAGCCTGAGGCTCTGACCAGAGTCAAGTCAAATCCTAGACATTAAGTACAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF8FFFFFFF
@SRR6575259.5 5/2
ACTGCATATTGTTACTGATTTTTTTCAATACACCCCACTGTTGTTAGGTAAACAGTTGTATATATAATATATACTAGACACACCTTTGCACACCGTGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6575259_1.fastq

Printing command:
fastqc --outdir SRR6575259_1.fastq

Analysis complete for SRR6575259_1.fastq

Processing SRR6575259_2.fastq

Printing command:
fastqc --outdir SRR6575259_2.fastq

Analysis complete for SRR6575259_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 215M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 108M Oct 12 19:41 SRR6575259_1.fastq
-rw-r--r--   1 kkarri waxmanlab 108M Oct 12 19:41 SRR6575259_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:44 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================